ISIS Reflectometry Interface¶

Runs tab¶

This section describes the different elements in the Runs tab.

Menu bar¶

The Reflectometry menu provides access to the following functionality:

Action	Effect
Open Table	Opens a valid TableWorkspace in the Processing Table for processing.
New Table	Discards the current contents of the Processing Table presenting a blank table.
Save Table	Saves the current contents of the Processing Table to the TableWorkspace it came from. If no such workspace already exists, a new one can be created.
Save Table As	Saves the current contents of the Processing Table to a new TableWorkspace.
Import .TBL	Opens a LoadTBL dialog, enabling you to load a .tbl file into a TableWorkspace.
Export .TBL	Opens a SaveTBL dialog, enabling you to save a TableWorkspace to a .tbl file.
Options	Opens the Options menu.
Slit Calculator	Opens the slit calculator: a tool to help calculate the correct geometry for the instruments’ slits. It’s powered by the CalculateSlits algorithm.

The Edit menu provides access to the same actions found in the tool bar. These are documented in the Tool Bar section of this document.

Processing Table¶

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 tool bar containing various actions for manipulating the processing table.

Below the table is a progress bar, which shows the current progress of any processing that is in progress. And at the bottom, near the Process button is the processing instrument selector. The processing instrument is used to help identify the correct data to load when processing runs.

While processing, any runs that have been successfully processed will have their row highlighted green. Any groups that have been post-processed successfully will also be highlighted. Starting a new reduction will clear all highlighted rows and groups.

If reduction is paused and then resumed again, the interface will check if any data in previously processed rows and groups had been manually changed in between. If data within a row has been altered, the row and its containing group will be reprocessed. If rows are added or removed from a group, the group will need to be processed again as well. Deleting or renaming the output workspaces for processed rows or groups will cause only that item to be processed again. It is also possible to change the selection of rows and groups and doing so will process new data items while ignoring any deselected ones.

Next to the Process button there is a checkbox which allows enabling and disabling output to an ipython notebook. If the checkbox is enabled, a dialog window will ask for a save location for the notebook after processing is complete. A generated notebook contains python code to repeat the processing steps and output relevant plots.

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.

Tool Bar¶

This table details the behaviour of the actions in the tool bar, from left to right.

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.
Expand Selection	Expands your selection such that the group containing the row you have selected is selected.
Expand Groups	Expands all currently collapsed groups in the table, revealing their individual runs.
Collapse Groups	Collapse all currently expanded groups in the table, hiding their individual runs.
Plot Selected Rows	Creates a plot of the IvsQ workspaces generated by any of the selected rows.
Plot Selected Groups	Creates a plot of the stitched IvsQ workspaces generated by any of the selected groups.
Insert Row	Adds a new row after the first selected row, or at the end of the group if a group was selected. If nothing was selected the new row is appended at the end of the last group.
Insert Group	Adds a new group after the first selected group, or at the end of the table if no groups were selected.
Group Rows	Takes all the selected rows and places them in a group together, separate from any other group.
Copy Rows	Copies the selected rows to the clipboard. In the clipboard, each column’s value is separated by a tab, and each row is placed on a new line.
Cut Rows	Copies the selected rows, and then deletes them.
Paste Rows	Pastes the contents of the clipboard into the selected rows. If no rows are selected, new rows are inserted.
Clear Rows	Resets the cells in any selected rows to their initial value, in other words, blank.
Delete Row	Deletes any selected rows. If no rows are selected, nothing happens. If the single row of a group is selected for deletion, the group will also be deleted.
Delete Group	Deletes any selected Groups. If no groups are selected, nothing happens.
What’s This	Provides guidance on what various parts of the interface are for.

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.

Description Based Search Transfer¶

Description based search transfer uses the descriptions associated with raw files from the experiment.

If a run’s description contains the text in 0.7 theta, or th=0.7, or th:0.7, 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:

• Any runs with the same description, excluding their theta value, will be placed into the same group.
• Any runs with the same description, including their theta value, will be merged into a single row, with all the runs listed in the Run(s) column in the format, 123+124+125.

Measure Based Search Transfer¶

Measure based search transfer uses the log-values within nexus files from the experiment to assemble the batch. Since the files themselves are required, not just the overview metadata, the files must be accessible by mantid. One way of doing this is to mount the archive and set the user property icatDownload.mountPoint to your mount point. It may end up looking something like this icatDownload.mountPoint=/Volumes/inst$. Alternately, you can download the files to your local disk and simply add that directory to the managed search directories in Manage User Directories.

• Any runs with the measurement_id log, will be placed into the same group.
• Any runs with the same measurement_id and the same measurement_subid logs, will be merged into a single row, with all the runs listed in the Run(s) column in the format, 123+124+125.

Failed transfers¶

When transferring a run from the Search table to the Processing table there may exist invalid runs. For example, if a Measure-based run has an invalid measurement id. In the image below we select three runs from the Search table that we wish to transfer to the 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 the Search table.

Hovering over the highlighted run with your cursor will allow you to see why the run was invalid.

Autoprocess¶

The Autoprocess button allows fully automatic processing of runs for a particular investigation. Enter the instrument and investigation ID and then click Autoprocess to start. This then:

• Searches for runs that are part of the investigation the id was supplied for.
• Transfers any initial runs found for that investigation from the Search table into the Processing table and processes them.
• Polls for new runs and transfers and processes any as they are found.

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.

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 an appropriate filtering algorithm (FilterByTime for uniform even, uniform and custom slicing, FilterByLogValue for log value slicing). 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, the interface will load the runs within that group as histogram workspaces and no event analysis will be performed for that group. A warning message will be shown when the reduction is complete indicating that some groups could not be processed as event data.

The four slicing options are described in more detail below:

• Uniform Even - The interface obtains the start and end times of the run and divides it into a specified number of evenly-sized slices. For example given a run of duration 100 seconds, specifying 4 uniform even slices will produce slices with ranges of 0 - 25, 25 - 50, 50 - 75 and 75 - 100 seconds respectively.
• Uniform - The interface obtains the start and end times of the run and divides it into several slices of a specified duration. If the total duration does not divide evenly by the slice duration, then the last slice will be shorter than the others. For example, given a run of duration 100 seconds, specifying slices of duration 30 seconds will produce slices with ranges of 0 - 30, 30 - 60, 60 - 90 and 90 - 100 seconds respectively.
• Custom - This takes a list if comma-separated numbers that indicate the start and end of each time slice. There are different possibilities:
  • If a single number is provided, e.g. 100, the interface will extract a single slice starting at the start of the run, and ending at 100 seconds.
  • If two numbers are provided, e.g. 100, 200, the interface will extract a single slice starting 100 seconds after the start of the run and stopping at 200 seconds after the start of the run.
  • If more than two numbers are provided, e.g. 100, 200, 300, the interface will extract two slices, the first one starting at 100 seconds after the start of the run and ending at 200 seconds after the start of the run, and the second one starting at 200 seconds and ending at 300 seconds.
• LogValue - Like custom slicing this takes a list of comma-separated numbers and are parsed in the same manner as shown above. The values however indicate the minimum and maximum values of the logs we wish to filter rather than times. In addition, this takes a second entry ‘Log Name’ which is the name of the log we wish to filter the run for. For example, given a run and entries of 100, 200, 300 and proton_charge for slicing values and log name respectively, we would produce two slices - the first containing all log values between 100 and 200 seconds, the second containing all log values between 200 and 300 seconds.

Workspaces will be named according to the index of the slice, e.g IvsQ_13460_slice_0, IvsQ_13460_slice_1, etc.

Settings tab¶

The Settings tab can be used to specify options for the reduction and post-processing. These options are used by the interface to provide argument values for the pre-processing, processing and post-processing algorithms. Each of these respectively refer to the following algorithms:

• CreateTransmissionWorkspaceAuto (applied to Transmission Run(s)).
• ReflectometryReductionOneAuto, main reduction algorithm.
• Stitch1DMany (note that at least a bin width must be specified for this algorithm to run successfully, for instance Params=”-0.03”).

Note that when conflicting options are specified for the reduction, i.e. different values for the same property are specified via the Settings tab and the Options column in the Runs tab, the latter will prevail. Therefore, the ReflectometryReductionOneAuto settings should be used to specify global options that will be applied to all the rows in the table, whereas the Options column will only be applicable to the specific row for which those options are defined.

The Settings tab is split into two sections, Experiment settings and Instrument settings. The former refers to variables set mostly by the user, while the latter refers to variables set by the instrument used to perform the reduction. Both have a Get Defaults button that fills some of the variables with default values. For experiment settings, these are pulled from the ReflectometryReductionOneAuto algorithm whereas for instrument settings, they are pulled from the current instrument being used in the run.

If either the Experiment or the Instrument settings sections are unchecked, this will disable all the of the entries for each respective section. In addition, the reduction will not make use of the values from any of the disabled entries.

Save ASCII tab¶

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].

When I try to process I get an error: “Invalid value for property Filename (list of str lists) ...”¶

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.

When I try to process I get an error: “Error encountered while stitching group ...”¶

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 Stitch1DMany text box in the 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".

When I try to process I get an error: “Invalid key value pair, ‘...’”¶

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".

When I try to process I get an error: “Invalid value for property ... Can not convert “False/True” to boolean”¶

This occurs when a boolean property is set to “True” or “False”. Please, use 1 or 0 instead.

The Open Table menu doesn’t do anything¶

The Open Table menu contains a list of valid table workspaces to open in the processing table. If a workspace is not compatible, it will not be listed. So, if there are no compatible workspaces the Open Table menu will be empty.

My IvsQ workspaces are not being stitched correctly¶

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.

An easy way to select all the rows in the same group for stitching is to select one of the rows you want stitched, and then in the menu bar select Edit -> Expand Selection. This will select the group your row is in. If you have another row that you would like to add to the group, you can do this easily by adding it to the selection, and then in the menu bar selecting Edit -> Group Selected.

The Save Table option does not output a .TBL file¶

In the old interface (ISIS Reflectometry) the “Save Table” and “Save Table as..” options were used to output a .TBL file into a directory of your choice. This functionality is now provided by the “Export .TBL” option in the Options Menu. This will allow you to save a .TBL file to a directory of your choice. The “Save Table” option in the Options menu now provides a way for you to save the processing table in a TableWorkspace where the name of the TableWorkspace is provided by the user.

Categories: Interfaces | Reflectometry