Table of Contents
This user interface allows for batch processing of data reduction for reflectometry data. The actual data reduction is performed with ReflectometryReductionOneAuto. Wherever possible, this interface attempts to use reasonable defaults, either loaded from the instruments’ parameter files, or calculated from the provided data, to minimise the amount of user input required. This interface also strives to be transparent, making it clear how your data is being processed, and easy to adjust any of the options used.
Integration with data archives is also provided, allowing for data to be located and prepared for reduction automatically.
Information on how to resolve common problems can be found in the Troubleshooting section of this document.
To follow this example you will need the ISIS reflectometry example materials:
These can be downloaded as part of the ISIS example data.
Once they are downloaded, place the nxs files in one of Mantid’s user directories. To see a list of directories, click on File -> Manage User Directories.
Open either MantidWorkbench or MantidPlot, and open the ISIS Reflectometry interface from the menu: Interfaces -> Reflectometry -> ISIS Reflectometry
First, we want to enter the runs that we will process into the table. Enter the values as shown in the figure below. Just the run number and the angle is the minimum requirement.
Tip
You can use the Toolbar or Keyboard Shortcuts to edit the table, e.g. Tab between cells, Enter to add a new row, Ctrl-I to insert a child row.
Run numbers and angles entered into the runs table
Let’s process the first group, which consists of the first two rows of the
table (13460 and 13462). Select the group we want to process, and then click on
Process.
The runs table after the first group has been processed with default settings
The rows within the group should turn yellow (probably very briefly) to indicate that they are processing, and then green when they have completed. Once both rows have been processed, the group will be post-processed and it will also turn green. The Q min, Q max and dQ/Q cells will also be updated with the values that were calculated in the reduction.
Tip
If a row or group turns blue, it has an error. Hover over the row to see the error message and consult the Troubleshooting section of this document for guidance on fixing it.
The above is a minimal reduction. We also want to use some transmission runs to correct this data. We could enter these into the runs table but instead we will use the Experiment Settings tab to set them as defaults for all runs. We will also set the limits and resolution for the final rebinning in Q, and output the debug workspaces.
Enter the following information on the table on the Experiment Settings tab, and tick the Debug option. Then re-process the group.
Editing experiment settings
You should now have several workspaces in the ADS. Amongst them should be:
| Workspace | Description |
|---|---|
| TOF_13460 | This is the data before processing. The X axis is time of flight in
 . |
| IvsQ_13460 | This is the output workspace of ReflectometryReductionOneAuto. The X axis is momentum transfer in Å-1. |
| IvsQ_13460_13462 | This workspace is the result of stitching IvsQ_13460 and IvsQ_13462 together using Stitch1DMany. The X axis is momentum transfer in Å-1. |
| IvsLam_13460 | This is the wavelength output workspace of ReflectometryReductionOneAuto. The X axis is wavelength in Å. It is only output if the Debug option is ticked. |
| TRANS_13463_13464 | This is a transmission run, created by running CreateTransmissionWorkspace on TOF_13463 and TOF_13464. The X axis is wavelength in Å. |
For convenience, the interface provides tools to easily plot the main
outputs. The plot-rows 
button plots the reduced runs
(i.e. IvsQ_binned_13460 and IvsQ_binned_13462) for the selected row(s),
and/or all rows in the selected group(s). The plot-groups 
button
plots the stitched output for the selected group(s)
(i.e. IvsQ_13460_13462).
Plotting the results of the reduction
The main window contains one or more “Batches”, which are shown as vertical tabs on the left. Each Batch contains a group of settings tabs (Runs, Event Handling, Experiment, Instrument and Save ASCII). Together, these provide all of the settings for a particular reduction.
Batch tabs on the left contain all of the reduction settings for a particular batch of runs
Using multiple batches is useful when users need to apply different options to runs measured during the same experiment. For instance, if some runs need to be analyzed with a wavelength range of LambdaMin=1, LambdaMax=17 but others need a wavelength range of LambdaMin=1.5, LambdaMax=15, users may want to enter the first set of runs in the processing table in one batch and the second set in the processing table in another batch, and update the settings in each batch accordingly. The interface will use the settings from the relevant batch to reduce runs in that batch’s processing table.
This section describes the different elements in the Runs tab.
The runs tab
The processing table is where the bulk of the work takes place. It is used to specify which runs to process, the properties that should be used to process them, and how the different runs should be joined together.
Each row represents a single reduction (i.e. execution of ReflectometryReductionOneAuto), and belongs to a group. Rows that are grouped together will have their output stitched together using Stitch1DMany.
Above the processing table is a Toolbar containing various actions for manipulating the processing table, and a filter bar to allow filtering of the table by group or run name. Various Keyboard Shortcuts are available to help with quickly editing the table.
To process, simply select the rows or groups you want to process and click
Process . Alternatively, if nothing is selected, the entire table
will be processed.
Below the table is a progress bar, which shows the current progress of any processing that is in progress. When processing the entire table, this will show the percentage of the entire table that is complete. When processing a selection it will show the percentage of that selection that is complete.
The processing table
Rows or groups that are currently processing will be highlighted in yellow, and those that are successfully complete will be highlighted in green. Note that groups that only have a single row do not have any stitching to do so will not be processed and therefore will not turn green. If processing fails for any reason, the row/group will be highlighted in blue and you can over over it to see a tooltip displaying the error message.
Editing any settings that may change the outputs will reset the state for all rows and groups. If any rows are added to or removed from a group, the group’s state will be reset. Deleting any of the mandatory output workspaces will also reset the relevant row or group states. Note however that if you rename a workspace, the interface will track it, so it will remain associated with its original row or group.
If reduction stops and is then resumed, the interface will re-process any rows
and groups within the current selection that have not been processed, or whose
state has been reset. If you manually select rows/groups that have an error
then they too will be reprocessed. However if you process the entire table
(i.e. click Process when nothing is selected), rows/groups that
have errors will not be reprocessed - you can manually select all rows in
the table if you want to reprocess them.
Note: The interface cannot be closed while runs are being processed. To
close the interface, you must first stop the reduction by clicking on the
Pause 
button.
The processing table contains the following columns:
| Column Title | Required? | Description |
|---|---|---|
| Run(s) | Yes | Contains the sample runs to be processed. Runs may be given as run numbers or workspace names. Multiple runs may be added together by separating them with a + or ,. Example: 1234+1235+1236 Note that if a workspace name contains + or , you must enter it in quotes, e.g. "TOF_1234+1235+1236" |
| Angle | Yes | Contains the angle used during the run, in degrees. If left blank, ReflectometryReductionOneAuto will calculate theta using SpecularReflectionCalculateTheta. Example: 0.7 |
1st Trans Run(s) 2nd Trans Run(s) |
No | Contains the transmission run(s) used to normalise the sample runs. To specify two transmission runs, enter them in each input box. Note that as per the Run(s) column, you can sum multiple runs for each input by entering multiple values separated by + or ,. If left blank, the sample runs will be normalised by monitor only. Example: 1234,1235 |
| Q min | No | Contains the minimum value of Q to be used in Å−1. Data with a value of Q lower than this will be discarded. If left blank, this is set to the lowest Q value found. This is useful for discarding noisy data. Example: 0.1 |
| Q max | No | Contains the maximum value of Q to be used in Å−1. Data with a value of Q higher than this will be discarded. If left blank, this is set to the highest Q value found. This is useful for discarding noisy data. Example: 0.9 |
| dQ/Q | No | Contains the resolution used when rebinning output workspaces. If left blank, this is calculated for you using the NRCalculateSlitResolution algorithm. This value is negated so that Logarithmic binning can be applied for the IvsQ workspace. If you desire linear binning then you may negate the value in the processing table and a linear binning will be applied. Example: 0.9 |
| Scale | No | Contains the factor used to scale output IvsQ workspaces. The IvsQ workspaces are scaled by 1/i where i is the value of this column. Example: 1.0 |
| Options | No | Contains options that allow you to override ReflectometryReductionOne’s properties. To override a property, just use the property’s name as a key, and the desired value as the value. Options are specified in key=value pairs, separated by commas. Values containing commas must be quoted. Options specified via this column will prevail over options specified in the Settings tab. Example: RegionOfDirectBeam="0,2", Params="1,2,3" |
This table details the behaviour of the actions in the tool bar, from left to right.
The runs table toolbar
| Action | Effect |
|---|---|
| Process |
Processes the selected runs, or, if no runs are selected, all of the runs in the table. When a group is selected, runs belonging to the same group are stitched together. |
| Pause |
Pauses processing any selected runs. Processing may be resumed by clicking on the ‘Process’ button. If the selection has changed, the new selection will be processed. |
 Expand Groups |
Expand all groups so that you can see all child rows. |
 Collapse Groups |
Collapse all groups to hide all child rows. |
| Plot Selected
Rows
Rows |
Creates a plot of the IvsQ workspaces generated by any of the selected rows (or all child rows of the selected groups). |
| Plot Selected
Groups |
Creates a plot of the stitched IvsQ workspaces generated by any of the selected groups. |
 Insert Row |
Inserts a new child row into the selected group |
 Delete Row |
Deletes any selected rows. If no rows are selected, nothing happens. |
 Insert Group |
Adds a new group after the first selected group, or at the end of the table if no groups were selected. |
 Delete Group |
Deletes any selected Groups. If no groups are selected, nothing happens. |
 Copy Rows |
Copies the selected rows or groups into the clipboard. |
 Paste Rows |
Pastes the contents of the clipboard onto the selected rows or groups. For groups, if no destination is selected the they will be pasted as new groups at the end of the table. Rows must always be pasted onto a destination selection of the same size. |
 Cut Rows |
Copies the selected rows, and then deletes them. |
The following keyboard shortcuts are available for editing in the the runs table.
| Shortcut | Action |
|---|---|
| F2 | Edit the current cell |
| Esc | Cancel editing |
| Tab | Next cell |
| Shift-Tab | Previous cell |
| Enter | Edit the next row / append a new row |
| Ctrl-I | Insert child row |
| Ctrl-X | Cut |
| Ctrl-C | Copy |
| Ctrl-V | Paste |
| Delete | Delete the selected rows/groups |
| Up/Down | Select next/previous row |
| Shift-Up/Shift-Down | Extend selection to next/previous row |
| Ctrl-A | Select all |
The search interface
To search for runs, select the instrument the runs are from, enter the id of the investigation the runs are part of, and click on Search.
In the table below, valid runs and their descriptions will be listed. You can
then transfer runs to the processing table by selecting the runs you wish to
transfer, and click the Transfer 
button. You can also
right-click on one of the selected runs and select Transfer in the context
menu that appears.
Search transfer uses the descriptions associated with raw files from the experiment.
If a run’s description contains the text th=0.7 at the end of the description then the interface will deduce that the run’s angle (also known as theta), was 0.7, and enter this value into the angle column for you. This holds true for any numeric value.
When multiple runs are selected and transferred simultaneously, the interface will attempt to organise them appropriately in the processing table. The exact behaviour of this is as follows:
When transferring a run from the Search table to the Processing table there may exist invalid runs. For example, where theta could not be found or is zero. In the image below we have selected four runs from the Search table that we have transfered to the processing table.
Selecting runs from search table to transfer to processing table
Attempting to transfer an invalid run will result in that run not being transferred to the processing table. If the transfer was not successful then that specific run will be highlighted in blue in the Search table. Hovering over the highlighted run with your cursor will allow you to see why the run was invalid.
The interface provides Autoprocessing, which allows fully automatic processing of runs for a particular investigation. Enter the instrument and investigation ID and then click Autoprocess to start. This then:
If the investigation has not started yet, polling will begin straight away and the Processing table will remain empty until runs are created.
Like the Process button in the Processing table, the Autoprocess button will be disabled while autoprocessing is in progress. If autoprocessing has been paused, the button will be enabled again. Clicking Autoprocess again will resume processing from where it left off.
Rows that do not contain a valid theta value will not be included in autoprocessing - they will be highlighted as failed rows in the Search table. The error message will be displayed as a tooltip if you hover over the row. These rows can be transferred manually by first pausing autoprocessing and then selecting the rows and clicking Transfer.
Successfully reduced rows are highlighted in green. If a group has been post-processed successfully then it is also highlighted in green. If the group only contains a single row then post-processing is not applicable, and the group will be highlighted in a paler shade of green to indicate that all of its rows have been reduced successfully but that post-processing was not performed.
If row or group processing fails, the row will be highlighted in blue. The error message will be displayed as a tooltip if you hover over the row. Failed rows will not be reprocessed automatically, but you can manually re-process them by pausing autoprocessing, selecting the required rows, and clicking Process.
The Processing table is not editable while autoprocessing is running but can be edited while paused. Any changes to a row that will affect the result of the reduction will cause the row’s state to be reset to unprocessed, and the row will be re-processed when autoprocessing is resumed. You can also manually process selected rows while autoprocessing is paused using the Process button.
Rows can be deleted and new rows can be added to the table while autoprocessing is paused. Use the buttons at the top of the Processing table, or manually transfer them from the Search table. They will then be included when you resume autoprocessing.
If workspaces are deleted while autoprocessing is running, or before resuming autoprocessing, then affected rows/groups will be reprocessed if their mandatory output workspaces no longer exist. If you do not want a row/group to be reprocessed, then you must first remove it from the table. Deleting interim workspaces such as IvsLam will not cause rows to be reprocessed.
Changing the instrument, investigation id or transfer method while paused and then clicking Autoprocess will start a new autoprocessing operation, and the current contents of the Processing table will be cleared. You will be warned if this will cause unsaved changes to be lost.
The live data section
The Live data section on the Runs tab allows you to start a monitoring algorithm that will periodically load live data from the instrument, given by the update interval spin box, and reduce it with ReflectometryReductionOneAuto. It outputs two workspaces, TOF_live for the original data and IvsQ_binned_live for the reduced data.
Live values for ThetaIn and the slit gaps are checked and used each time the reduction runs. Other algorithm properties are taken from Group 1 on the Settings tab. Make any changes you want to the settings and press Start monitor to begin monitoring. Note that any changes to the settings will not be updated in the live data reduction unless you stop and re-start monitoring.
You can stop monitoring at any time using the Stop monitor button or by cancelling the algorithm from the Algorithm progress dialog. If you close the interface, monitoring will continue running in the background. You can cancel the MonitorLiveData algorithm from the Algorithm progress dialog.
If MonitorLiveData stops due to an error, the Start monitor button will be re-enabled so that it can be re-started from the Interface.
Note that if you close and re-open the Interface, the link to any running monitor algorithm will be lost. You will not be able to start a new version of the monitor due to a clash in the output names. Stop the algorithm from the Algorithm process dialog and re-start it from the new instance of the Interface to re-link it.
Live data monitoring has the following requirements:
The event handling tab
The Event Handling tab can be used to analyze event workspaces. It contains four text boxes for specifying uniform even, uniform, custom and log value slicing respectively. Each of these slicing options are exclusive, no more than one can be applied. If the text box for the selected slicing method is empty no event analysis will be performed, runs will be loaded using LoadISISNexus and analyzed as histogram workspaces. When this text box is not empty, runs will be loaded using LoadEventNexus and the interface will try to parse the user input to obtain a set of start and stop values. These define different time slices that will be passed on to the filtering algorithms (GenerateEventsFilter and FilterEvents). Each time slice will be normalized by the total proton charge and reduced as described in the previous section. Note that, if any of the runs in a group could not be loaded as an event workspace, you will get an error message and the reduction will not be performed.
The four slicing options are described in more detail below:
Workspaces will be named with a suffix providing information about the slice, e.g IvsQ_13460_slice_50_75, IvsQ_13460_slice_75_100, etc.
The experiment Settings tab
The Experiment Settings and Instrument Settings tabs can be used to specify options for the reduction and post-processing releting to a specific experiment. The Experiment settings are variables that are mostly set by the user, whereas the Instrument Settings are variables relating to the instrument used to perform the reduction. Both are populated with default values for the current instrument. The Restore Defaults button allows you to revert the settings to the default values for the instrument.
The majority of these options are used by the interface to provide argument values for the pre-processing and reduction steps, which are handled by the algorithm: ReflectometryISISLoadAndProcess
The exception is Output Stitch Params, which is used for the final stitching done by the algorithm Stitch1DMany. Note however that if a bin width is not provided, for instance Params="-0.03", then -dQ/Q will be used, if specified; otherwise a default value will be calculated from the slits, if possible.
Note that when conflicting options are specified for the reduction, i.e. different values for the same property are specified via one of the settings tabs and the cells in the Runs tab, the latter will take precedence. Therefore, the Settings tabs should be used to specify global options that will be applied to all the rows in the table, whereas the row values will only be applicable to the specific row for which those options are defined.
The Experiment Settings tab allows some options to be specified on a per-angle basis, that is, to specify defaults that will apply only to runs with a specific angle. Note that matching angles are searched for within a tolerance of 0.01. In the per-angle defaults table, you can also specify a “wildcard” row, which will apply to all runs that don’t also have a matching angle - just leave the angle blank to create a wildcard row. Only one wildcard row may exist.
The per-angle defaults table
Entries in the per-angle defaults table are similar to the table on the Runs tab. Default transmission runs can be specified and each input can take a single run/workspace or a number of runs/workspaces that will be summed before processing. Specific spectra of interest can be specified for the input runs and separate spectra, if required, can be specified for the transmission runs - if the latter are not specified then the Run Spectra will also be used for the transmission runs. If both a First and Second tranmission input is specified, then they will be stitched using the options specified.
Transmission run options
The Save ASCII tab allows for processed workspaces to be saved in specific ASCII formats. The filenames are saved in the form [Prefix][Workspace Name].[ext].
The save ASCII tab
| Name | Description |
|---|---|
| Save path | At present this dialog doesn’t have a standard file dialog so that path must be filled in manually. The path must already exist as this dialog doesn’t have the ability to create directories. As the naming of files is automatic, the path must also point to a directory rather than a file. |
| Prefix | The prefix is what is added to the beginning of the workspace name to create the file name. No underscore or space is added between them so they must be manually added. |
| Filter | This can be specified to filter out workspaces in the workspace list whose name does not match that of the filter text. |
| Regex | Checking this option allows a regular expression to be used for filtering workspace names. |
| List Of Workspaces | The left listbox will contain any workspaces loaded into mantid (excluding group and table workspaces). Double clicking on one will fill the right list box with the parameters it contains. This listbox supports multi-select in order to allow for multiple workspaces to be saved out at the same time with the same settings. |
| List Of Logged Parameters | The right listbox starts out empty, but will fill with parameter names when a workspace in the left listbox is double clicked. This listbox supports multi-select in order to allow for the save output to contain multiple parameter notes. |
| File format | This dialog can save to ANSTO, ILL cosmos, 3-column, and a customisable format. It doesn’t save from the main interface’s table, but from workspaces loaded into mantid. All algorithms are also available as save algorithms from mantid itself. |
| Custom Format Options | When saving in ‘Custom’ this section allows you to specify if you want a Title and/or Q Resolution column as well as specifying the delimiter. |
| Automatic Save | Automatically save the main output workspace for groups in the runs table. Note that the stitched group output will be saved if there is one or, for a single-row group, the IvsQ_binned row output will be saved instead. |
This occurs when Mantid is unable to load a run. If the run was given as a workspace name, check the spelling. If the run was given as a number, check that the run number is correct. If the run number is incorrect, check the number given in the Run(s) or Transmission Run(s) columns. If the run number is correct, check the instrument named in the error message is correct. If the instrument is incorrect, check that the processing instrument selector (at the bottom right of the interface) is correct.
If the run still isn’t loading check Mantid’s user directories are set correctly, and that the desired run is in one of the given directories. To manage the user directories, open File -> Manage User Directories.
This occurs when Mantid is unable to stitch a group. Please check that at you have specified at least the bin width. This can be done either by setting a value in column dQ/Q before processing the data, or by using the Output Stitch Params text box in the Experiment Settings tab to provide the Params input property like this: Params="-0.03" (you may want to replace 0.03 with a bin size suitable for your reduction). Note that the “-” sign in this case will produce a logarithmic binning in the stitched workspace. For linear binning, use Params="0.03".
This occurs when the contents of the options column are invalid. Key value pairs must be given in the form key = value, and if the value contains commas it must be quoted, like so: key = "v,a,l,u,e".
This occurs when a boolean property is set to “True” or “False”. Please, use 1 or 0 instead.
Stitching is controlled by the group a row is in. For stitching to occur, the rows must be in the same group, and be processed simultaneously. To select all rows in a group, just select the group itself - its child rows are implicitly selected.
Categories: Interfaces | Reflectometry