SAXS / WAXS Data & Analysis

Index

Data collection on the SAXS/WAXS beamline is normally performed using the scatterBrain IDL program developed in house. This program has been developed to provide a more intuitive and user friendly interface and is also designed to provide greater flexibility in automated scans. scatterBrain does not inhibit the time resolution of the detectors, allowing them to be run at their full acquisition rate and removing the need for a different interface for time-resolved data collection. A scatterBrain wiki (currently only available on site at the synchrotron) has been established to proivde help information and to report and track bugs.

Historically, data was collected on the SAXS-WAXS beamline using a slightly modified version of the SAXS15ID program developed at ChemMat CARS as the user interface and control program. This was highly successful, although it was not overly user friendly and a slight delay (1-2 seconds) in image processing hindered time resolution. Limited support for SAXS15ID remains available for legacy data that preceeds the availability of scatterBrain.

Data Retrieval

Experiments at the SAXS / WAXS beamline routinely generate considerable volumes of data and Users are expected to take a copy of their data at the end of their beamtime. Images from the Pilatus 1M SAXS detector and Pilatus 200K WAXS detector are approximately 4 MB and 1 MB respectively. As hundreds of images are routinely collected during each day of beamtime, Users typically require several gigabytes of storage for their data. When rapid image collection is used, e.g. time-resolved experiments, data volumes of above 50 GB can be expected. Please consider the options below prior to an experiment to ensure you are able to obtain a copy of the data set.

Local Data Collection at the Beamline

As very large data volumes can be expected we ask that Users bring a Windows-compatible external hard drive to take a copy of the data as this is considerably more efficient than using memory sticks or burning to DVD. External USB disk can be easily connected directly to the beamline computers if they are FAT32 or NTFS format.

Local Data Access Guide:

1. Plug in a Windows compatible drive, i.e. FAT32 or NTFS, into the front USB port of any Windows computer on the beamline.

2. Open ‘My Computer’, browse for your data for each detector used:

- Pilatus1M = X:\data\Cycle_YEAR_N\Username_proposalnumber\

- Pilatus200K (WAXS) = Y:\Cycle_YEAR_N\Username_proposalnumber\

- MAR165 = Z:\data\Cycle_YEAR_N\Username_proposalnumber\

3. Copy & Paste the data to your drive. Do NOT use ‘Cut’.

Remote Access to Data

Data for each experiment is stored at the synchrotron and are available online once archived. Data may be downloaded from the VBL by logging in and following the link to the Storage Gateway. Experiments are arranged by experiment number and date and you may download selected data or complete datasets. By default only the Principal Investigator for an experiment has access to this feature, however they may grant access to others.

When downloading data via SSL transfer, data will be downloaded as a single .tar file that will then need to be decompressed. This .tar file can be very large in size, often exceeding the 4GB file size limit of FAT32 drives. We recommend you download your data to an NTFS, ext2 or ext3 drive or partition by setting the download directory in your web browser, to avoid problems due to the 4GB file size limit. For Windows, we have found 7-Zip an effective freeware compression program, which is readily available online.

Remote Data Access Guide:

1. Go to the VBL at https://vbl.synchrotron.org.au in a web browser and log in with your username (email address registered in the Portal) and password.

2. Select the ‘Storage Gateway’ link. A list of experiments to which you have access will be shown, arranged by date. If you cannot see your experiment you may not have access (only the Principal Investigator has access by default), or the data may not yet be archived.

3. Select an experiment and a method of data transfer. The most accessible protocol is the ‘SSL Transfer’ as other options may need special arrangements set up.

4. Navigate to the folder you wish to download and select ‘Download All’ to download all files and subfolders. To download specific files, select ‘Download Selection’ instead. The data will download to the default location set in your web browser. If you need to save data to a different location change the download location for your browser. If you are downloading to a FAT32 drive the download may be interrupted if downloading more than 4 Gb.

5. Decompress the .tar file once it has finished downloading. 7-zip is a freeware compression program that may be used to decompress .tar files in windows.

Data Analysis

Data is collected as .tif images. The profiles shown in scatterBrain at the beamline are not generally saved. It is expected that processing, e.g. radial integration & plotting scattering profiles, will be done by Users after leaving the synchrotron using another version of scatterBrain. This ensures that the full data set is available for processing and study after leaving the synchrotron, although beamline staff may be contacted for assistance if required.

The scatterBrain program is available locally at the beamline and on the website below. scatterBrain is an IDL program. In the past this meant that Users who do not have a copy of IDL needed to download the (freely available) IDL Virtual Machine from the ITT website as detailed below. However, we now provide a version with the IDL Virtual Machine built in. Simply download the program, unzip, and run the scatterBrainAnalysis.exe (Windows) or scatterBrainAnalysis.app (OSX). No installation required.

For more details, and to download the latest version of the scatterBrain Analysis Edition, refer to the SAXS Software Page.

The final version of SAXS15ID with Virtual Machine built in can be downloaded here. (zip, 34 MB). Note this is Windows only.

If you wish to use SAXS15ID with your own IDL installation the final version (3.299) of the SAXS15ID .sav file is available for downloading here (zip, 2.4 MB). It requires the IDL 8 Virtual Machine. (If you would prefer an IDL 7 compatible version, contact beamline staff who will build one for you.)

A manual for SAXS15 is available for downloading here (pdf, 4 MB).

Note the following is no longer necessary for most Users (as the Virtual Machine is now bundled with the download above):
Information on the open licence IDL Virtual Machine is available on the ITT web page. To download a copy of the program, you must register with the website and then follow the links in the Downloads page. The IDL download is approximately 250 - 350 MB depending on your operating system.

Additional Resources

An additional computer is provided for Users to inspect and assess their data to allow uninterrupted running on the main control computer. The additional PC has access to data collected during an experiment over the local network as soon as it is collected.

A standard suite of freeware SAXS analysis software, e.g. Fit2D, is also available on the beamline computers for processing and evaluating data during an experiment if necessary.

The User Manual for the SAXS / WAXS beamline is available for downloading here (pdf, 5 MB).

Troubleshooting

A few reported errors and fixes for scatterBrain are detailed below. If you are having problems that are not covered below please contact beamline staff.

Run-time error '5'

scatterBrain typically installs easily as a complete package from the .zip file. However on some Windows computers you may see the following error when you first attempt to run scatterBrain:

“Run-time error "5". Invalid procedure call or argument.”

If this occurs, the solution we recommend is to install IDL8 Virtual Machine on your Windows computer, and then run scatterBrain in the usual way from scatterBrain.exe. You can download IDL8-VM from Exelis at

http://www.exelisvis.com/ProductsServices/IDL/IDLModules/IDLVirtualMachine.aspx

You will need to register (free) prior to download. Make sure you use version8 as earlier versions will not work. We have not seen this effect on other operating systems.