Table of Contents
This interface is hidden and will likely be removed from the next release of mantid.
This custom interface integrates several tasks related to engineering diffraction. It provides functionality for calibration, focusing, and pre-processing of event mode data. Further extensions can be expected for future releases as it is under active development. Feedback is very much welcome. The following sections describe the different tabs or functionality areas of the interface.
This tab provides a graphical interface to calculate calibrations and visualize them.
It is possible to:
For the current calibration, the following parameters are displayed:
This calibration file output is a GSAS instrument parameters file (IPARM/PAR/PRM). The interface produces a calibration file containing all banks and in addition a calibration file for every individual bank. All the calibration files are written in the same directory.
With the help of Cropped Calibration user can also calibrate according to specific banks or by setting the Spectrum Numbers once the Cropped Calibration group box has been enabled.
The plot Calibrated Workspace check-box will enable user to plot vanadium curves and Ceria peaks. For Ceria peaks there will be two workspaces generated and plotted, one for each bank, whereas for a cropped calibration there will only be one workspace generated and plotted, depending on the selected bank or provided Spectrum IDs. The workspace contains difa, difc and tzero data which is then utilised to plot the Ceria peaks per bank, the graph will plot Peaks Fitted and TOF Straight Line for comparison. More information regarding the fit peaks can be found on the EnggFitPeaks documentation.
The calibration files are written into two different output directories. First, they are written to a user specific directory which for the ENGIN-X instrument on Windows systems is:
C:\EnginX_Mantid\<Username>\<RBNumber>\Calibration
On UNIX based platforms this path is:
~/EnginX_Mantid/<Username>/<RBNumber>/Calibration
They are also copied into a general (all) output directory:
C:\EnginX_Mantid\Calibration on Windows or
~/EnginX_Mantid/Calibration on UNIX platforms.
The calibration parameters for each bank are made available for user inspection in a workspace named engggui_calibration_banks_parameters which is updated when new calibrations are loaded or calculated.
These parameters are required to generate new calibrations:
The calibration process depends on several additional parameters and settings which can be modified in the Settings tab, see Settings for details.
Here it is possible to focus run files, by providing a run number or a range of run number to enable multi-run focusing, along with that the user may also select the files with the help of Browse button.
The focusing process uses the algorithm EnggFocus. In the documentation of the algorithm you can find the details on how the input runs are focused.
The interface will also create workspaces that can be inspected in the workspaces window:
Three focusing alternatives are provided:
Depending on the alternative chosen, the focusing operation will include different banks and/or combinations of spectra (detectors). The behavior for each option is as follows:
1. Normal focusing - All the selected banks and spectra present in the input runs are considered. The output focused workspace will be named with suffixes such as _bank_1, _bank_2, and so on
2. Cropped Focusing - All the banks are considered in principle but only a list of spectra provided manually are processed. The output focused workspace will be named with the suffix _cropped.
3. Texture Focusing - The banks are selected by a user-defined list of banks and corresponding spectrum numbers provided in a file. The output workspaces will be named with suffixes such as _texture_bank_1, _texture_bank_2, and so on. These suffixes are determined by the bank IDs given in the detector grouping file.
Cropped focusing and Texture focusing have been disabled by default to declutter the interface, but each section can be enabled simply by ticking the check-box next to Focus Cropped and Focus Texture.
For texture focusing, the detector grouping file is a text (csv) file with one line per bank. Each line must contain at least two numeric fields, where the first one specifies the bank ID, and the second and subsequent ones different spectrum numbers or ranges of spectrum numbers. For example:
# Bank ID, spectrum numbers
1, 205-210
2, 100, 102, 107
3, 300, 310, 320-329, 350-370
When a focus run process is being carried out, Focus Stop button will be enabled. Focus Stop button will allow the user to abort once the current focus run process has been completed. Inside the Result Log a warning message will be displayed with last successful run and total number of focus runs that could not be processed.
The focused data files are saved in NeXus format into the user specific and general directories (as with the calibration output files). That is the files are written into C:\EnginX_Mantid\User\<RBNumber>\Calibration and C:\EnginX_Mantid\Calibration on Windows, or ~/EnginX_Mantid/User/<RBNumber>/Calibration and ~/EnginX_Mantid/Calibration on UNIX platforms. See below for additional, optional outputs.
The run provided to focus can be for example 228061-228063, this will run all the files within the given range as long as the file directories are included in the User Directories. The user may also provide an input of 228061-3 or 228061, 228062, 2280623 which should work the same way.
If a red star sign is displayed next to the Browse Button, it is mostly likely because the file specified has not been found. Error message can be viewed by hovering over the red star sign.
Checking the availability of all the files can take some time, for this reason it is also possible that a file may not have been found but the red star sign has not been displayed. If you manage to click Focus before red sign is displayed, the interface will process the last valid focus run instead.
Under the output section, the user is provided with an option of plotting data in three different formats.
However, user may also change the Plot Data representation drop-down box while a run is being carried out. This will update the interface and plot workspace according to the new given input. For example, if a user has selected One Window - Replacing Plots and then decides to change it to One Window - Waterfall during a run, the interface will carry on by plotting Waterfall within the same window.
The user also has an option of saving GSS, XYE and OpenGenie formatted files by clicking the Output Files checkbox. This will generate three different files for each focused output workspace in Mantid. These files can be found with appropriate name within:
C:\EnginX_Mantid\<User>\<RBNumber>\Focus on Windows or
~/EnginX_Mantid/Foxus on UNIX systems.
The files are also copied to the general (all) output directory which is
C:\EnginX_Mantid\Focus on Windows
~/EnginX_Mantid/Focus under on UNIX systems
The Multiple Runs Focus Mode combo-box enables two alternative focus modes. Focus Individual Run Files Separately is the default option set, which allows user to run focus with multi-run files. Whereas the Focus Sum Of Files option merges all the multi-run number files together and applies the Focus Process to the merged file.
Warning
This is a new capability that is currently in a very early stage of definition and implementation. Not all options may be supported and/or consistent at the moment.
The focusing options can be applied directly to histogram data. For event mode experiments, the event data (which would be loaded as event workspaces in Mantid) need to be pre-processed.
The simplest pre-processing option is “regular time binning” which will produce a histogram data workspace (as a Workspace2D). The only parameter required is the bin width. The workspace will be named with the following convention:
When the input run file contains multiple workspaces (it would be loaded by Load as multiple EventWorkspace workspaces) the output workspace will be a group with the corresponding number of histogram workspaces, binned separately. This is the case when the input run file comes from a multi-period experiment. Note that the time bin can be a multiple of the pulse time.
A different way of pre-processing event data is by rebinning multi-period data by pulse times. In this case the input required is the time step for the binning (the x axis of the output will be time instead of time-of-flight). It is also possible to specify the number of periods that will be processed (starting from the first one). This type of pre-processing produces workspaces with the following naming convention:
Focussing uses the algorithms Rebin and RebinByPulseTimes to bin the data in different ways when converting event data into histogram data.
Warning
This is a new capability that is currently in a very early stage of definition and implementation. Not all options may be supported and/or consistent at the moment.
Warning
The input workspace must be converted into a focused file first. The steps to complete this are found here: Focus
The Fitting tab provides a graphical interface which fits an expected diffraction pattern and visualises them. The pattern is specified by providing a list of peak centre values where Bragg peaks are expected. These values can have units of either TOF of dSpacing but not both. The algorithm EnggFitPeaks is used to background fit peaks in those areas using a peak fitting function.
To use the Fitting tab, user is required to follow these steps:
These parameters are required to process Fitting successfully:
Once the Fit button has been clicked Mantid will process the data. Please wait until the Fitting process has completed. Upon completion you should be able to view the Fitting tab which will contain:
Within the Preview section a user is able to zoom-in or zoom-out as well as select, add and save peaks.
The interface will also generate workspaces that can be inspected in the workspaces window:
During the Fit process, EnggSaveSinglePeakFitResultsToHDF5 algorithm will be utilised to save engggui_fitting_fitpeaks_param TableWorkspace as a hdf5 file. There will one file per run, indexed by bank ID, and the file will be found in the Runs directory of the user’s output directory. If Fit All was run on multiple runs, then an additional file for all runs will be output, which is indexed first by run number and then by bank ID.
In the plots, the x or abscissa axis is in d-spacing units, which are more convenient for peak fitting than time-of-flight. However the run files and the focus files are normally stored as time-of-flight data. For this reason a conversion from the time-of-flight data to d-spacing is required. The conversion is performed using the current calibration of banks. The interface handles this internally and adds special sample logs to the fitting workspaces (engggui_fitting_single_peaks and engggui_fitting_focused_ws). By inspecting the sample logs of these workspaces. The conversion is performed using the GSAS equations, as calculated by the algorithm AlignDetectors
Once the fitting process has completed and you are able to view a focused workspace with listed expected peaks on the data plot, the Select Peak button should also be enabled. If the user choose to load the focus workspace or if fitting fails with the given peaks then the focused workspace will be plotted so that the user can select the peaks manually.
If you’ve run a fit but you can’t see the reconstructed peaks, make sure the checkbox Plot fitted peaks is checked - if the fit was successful, then clicking this should show the results. Equally, if you want to hide fitted peaks, just uncheck this box and they will disappear.
By clicking Select Peak button the peak picker tool can be activated. To select a peak simply hold Shift key and left-click on the graph near the peak’s center.
To get help selecting the center of the peak, you may set the peak width by left-click and drag horizontally, while holding Ctrl key as well. Users may also zoom-in to the graph by holding left-click and dragging a box on the plot, and zoom-out by left-clicking on the plot.
When user is happy with the center position of the peak, you may add the selected peak to Parameters list by clicking Add Peak button. User may rerun Fit process by clearing peaks list using Clear button and manually selecting peaking using Select Peak button or instead Save the peaks list in CSV file by clicking Save button.
User may plot single peak fitting workspace in separate window by using Plot To Separate Window button, if the engggui_fitting_single_peaks is available.
Warning
This is a new capability that is currently in a very early stage of definition and implementation. Not all options may be supported and/or consistent at the moment.
The GSAS tab provides a graphical interface to the Mantid algorithm GSASIIRefineFitPeaks. This allows users to perform GSAS-style fitting on their data from Mantid.
The user must input the following files:
.prm format.cif files are supportedThe following parameters are also required:
.gpx project here, which can be opened and inspected from the
GSAS-II GUIGSASIIscriptable.py. This directory will normally be called
GSASII, if GSAS-II was installed normallyOptionally, you may also supply:
To do a refinement, take the following steps:
123456_1) should appear in the
Run Number list in the Preview section. Click the label,
and the run will be plottedDuring the Fit process, EnggSaveGSASIIFitResultsToHDF5 algorithm will be utilised to save the fit results, and also the parameters used, as a hdf5 file. There will be one file per run, indexed by bank ID, and the file will be found in the Runs directory of the user’s output directory.
You can toggle the fitted peaks on and off with the Plot Fitted Peaks checkbox, remove runs from the list with the Remove Run button, and plot the run and fitted peaks to a larger, separate plot using Plot to separate window.
Controls several settings, including the input folders where the instrument run files can be found. Other advanced options can also be controlled to customize the way the underlying calculations are performed.
The calibration settings are organized in three blocks:
The input directories will be used when looking for run files (Vanadium and Ceria). They effectively become part of the search path of Mantid when using this interface.
The pixel (full) calibration file contains the calibration details of every pixel of all banks, as produced by the algorithm EnggCalibrateFull. A default pixel calibration file is provided with Mantid packages. This calibration has been produced for the Vanadium and calibration sample (Ceria) runs indicated in the name of the calibration file. Note that this calibration is currently subject to changes, as the fitting of peaks is being refined.
The Following advanced settings are available to customize the behavior of this interface:
Most of the functionality provided by this interface is based on the engineering diffraction Mantid algorithms (which are named with the prefix Engg). This includes EnggCalibrate, EnggCalibrateFull, EnggVanadiumCorrections, EnggFocus, EnggFitPeaks and several other algorithms, explained in detail in the following Mantid algorithms documentation pages.
Categories: Interfaces | Diffraction