The Files tool

To begin with METIS, fill in the box with the file stub. Then click the Pick image folder button. This will post the file selection dialog. Use that to select the folder containing the sequence of images measured at elastic and (non-)resonant incidence energies.

Make sure the boxes containing file name templates are filled in correctly. These are used to specify the patterns used for the various files written during the measurement. Getting these right is an important part of organizing the entire data ensemble in an interpretable way.

Finally, click the Fetch file lists button. This will fill up the lists of elastic energy and measurement images. Eventually, the lists will be filled in and METIS will be ready to go.

METIS, after fetching all the image files.

To aid in data visualization, the three controls at the top of the Files page should be set correctly. The two drop-down menus are used to indicate the element and edge of the absorber. You will be prompted for this based on information gleaned from the elastic energy file names

The element and edge selection dialog.

Finally, the Divide by 10 button is used to indicate how to interpret the energy value part of the image files names. In this example, the elastic energies are indicated by 189280, 189285, and so on. These integers are the incident energy multiplied by 10, i.e. 18928.0, 19828.5, and so on. Clicking this button to the correct state helps METIS interpret the file names correctly.

The templates used to recognize elastic and measurement images (as well as the scan file name for herfd and rxes modes) are simple substitution templates.

token	Replacement	Configuration parameter
%s	file stub, NbF5_Kb2 in this example
%e	elastic energy value
%i	incident energy value (rxes and herfd modes)
%t	tiff counter string	♦metis→tiffcounter
%c	energy counter	♦metis→energycounterwidth

Use the Configuration tool to set the parameters governing the %t and %c tokens. If set incorrectly, the Fetch file lists button will return with an error about not being able to find files matching the templates.

Having these file naming templates allows the user to store images from multiple measurements in the same folder on disk.

The %t is, in practice, usually something like 0001 – it is a counter that is used by EPICS areaDetector to number repeated exposures of the camera. The way the BLA spectrometer is used, this is rarely incremented, although the number of leading zeros might be changed. The %c token is used in rxes and herfd modes to relate an exposure during the energy scan to the index of that energy point in the scan file. For xes mode, this is the counter used for repeated exposures of the non-resonant XES image.

Once all the files have been loaded into METIS, click on the Mask icon in the side bar to go to the mask creation tool.

Visualizing individual images

Individual image files can be plotted by double clicking on a file name in either the elastic or image file list.

Double click on items in the lists to display the measured images.

Double clicking on an item in the elastic file list displays the raw image for that elastic measurement.

Double clicking on an item in the image file list displays the raw image for that XES measurement.

HERFD measurements

A HERFD measurement uses a scan file as well as a complete set of elastic and image files. Thus none of the controls for folders or templates are disabled in HERFD mode.

METIS's files tool in HERFD mode.

In a HERFD measurement, the image file list is typically longer than the elastic file list. An image file must be collected at each point in a XANES scan – typically 100 or so points. In this example, elastic images are measured every eV from 9429 to 9454 eV, a range that surrounds the Lα₁ peak at 9442 eV.

RXES measurements

An RXES measurement is structured a little differently from the other measurement types. In the case of RXES, the sequence of masks is the same set of files as the sequence of emission measurements. That is, the elastic part of each image will be processed into a mask then applied to the same sequence of images.

METIS's files tool in RXES mode.

In this case, a scan file is used to correlate image numbers with energies. There is a list of elastic files, but no separate list of image files.

A Pt RXES image at a low energy. This looks much like a normal elastic image.

A Pt RXES image in the middle of the image sequence. Here the fluorescence and the elastic line are quite close in energy. The processing must somehow distinguish between the elastic and fluorescence portions of the signal.

A Pt RXES image at the end of the image sequence. Here the elastic signal is again easily distinguished form the fluorescence signal. The mask processing chore is to reject the fluorescence portion and retain the elastic portion.

Processing individual files

You can use METIS to examine individual elastic image files by starting in mask mode.

METIS's files tool in individual image mode.

Most of the controls are disabled in mask mode and the Fetch file lists button is, instead, labeled Import image. Pressing this button will post a file selection dialog allowing you to import a single image file from the Pilatus. This will be displayed in the Elastic files list.

Note that the file naming templates are not used in mask mode, so the image file to be examined can have any name.

Also note that the Data tool is not available in this mode and that the Mask tool will likewise only consider one image file at a time.

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Xray::BLA and METIS are copyright © 2011-2014, 2016 Bruce Ravel and Jeremy Kropf – This document is copyright © 2016 Bruce Ravel

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