1. The DAWNSci Eclipse science usecases Jun Aishima Software Engineer Diamond Light Source Didcot, UK

2. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

3. Synchrotron AKA – cool word, but what does it mean? syn·chro·tron/ ˈ siNGkrə ˌ trän/ Noun:A cyclotron in which the magnetic field strength increases with the energy of the particles to keep their orbital radius constant. “They are machines which produce very strong light used for many different type of scientific experiments and sometimes other things.”

4. Diamond Light Source, Didcot, Oxfordshire, UK

5. (Video has been removed to allow the talk to fit into size guidelines – see http://www.diamond.ac.uk/Public/Multimedia/ Animations.html to view the animation) http://www.diamond.ac.uk/Public/Multimedia/ Animations.html

6. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

7. Detectors of Various flavors

8. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

9. …180 images The collected data may look like this…

10. When what you really want is this…

11. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

12. DAWN - Acquisition and Analysis with RCP @ Diamond Light Source Client server technology Communication with EPICS and hardware Scan mechanism www.opengda.org Jython and Python Visualisation Communication with external analysis Analysis tools Data read, write, convert Metadata structure Workflows www.dawnsci.org DAWN is a collection of generic and bespoke ‘views’ collated into ‘perspectives’. The perspectives and views can be used in part or whole in either the GDA or DAWN. Acquisition Analysis

13. Collaborative Approach Kichwa Coders Ltd. Science Working Group External Users Consultants Members Now an Eclipse project! https://projects.eclipse.org/projects/technology.dawnsci

14. ‘Shoulders of Giants’ AKA – didn’t think of everything RCP many of the core features, editors, toolbars, views, projects Ptolemy 2 (a version known as ‘Passerelle’) workflow and pipelining GEF for visualization of pipeline graphs Draw2D for 1D and 2D plotting (SWT XY Graph) Pydev for python/jython scripting layer used by the scientists HDF5 libraries for storing large data sets SWT/Jface – lazy viewers being used extensively for large trees and tables Apache, Eclipse-WST, springsource, JDK, and many more of course...

16. Did you see our poster yesterday, presented by Bahá? The DAWNSci Eclipse Project: How Eclipse Is Used for Science (Bahá El Kassaby) –Printed copies or PDF file available! Ask us!

17. Data in DAWNSci Example : Loading and Manipulating Data This example Columns of ASCII data Separated by tabs Read as 1D arrays Other format with a loader: srs, dat, flt, gff, mca, csv, xy, xye, txt, tif, tiff, cbf, img, ciff, mccd, edf, pgm, cor, bruker, jpg, jpeg, png, f2d, msk, mib, mar3450, pck3450, raw, mrc, gz, bz2, zip, h5, hd5, hdf5, nxs, nexus, hdf, mat Extension point to add more...

18. Demonstration – Visual Tools

19. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

20. The Processing pipeline Previous systems –Required much effort by the developer –User experience was too generic – not optimized for this purpose Simplify (coding), simplify (GUI), simplify (capabilities) Result: wide adoption and rapid development for several experimental techniques Developed by Jacob Filik at Diamond Available in DAWN

21. Non-crystalline diffraction Why Processing in DAWN?

22. Simple? Operation Calculation Error handling

23. Simple? Model Allow drag and drop Provide a button to open file dialog box Radio box in GUI Number box in GUI with limits Mouseover in GUI

24. Simple? File list Input Output List of processing steps Model

25. Demonstration of pipeline

26. 1.What is a light source and why do science there? 2.What data do you get at a synchrotron? 3.What do you do to the data? 4.How do DAWN and DAWNSci Eclipse help with this? 5.How do we use DAWN and DAWNSci Eclipse to analyze our data? 6.How can you use DAWN and DAWNSci Eclipse to analyze your data?

27. Create your own operations and pipelines! Create an operation – org.eclipse.dawnsci.analysis.api.operation extension point –Dataset operations – including lazy operations Create a model – if necessary –Any additional data required for the calculation –Reflection on data type and annotations are used to build the GUI for users to enter parameters

28. A lot of existing, reusable operations Sector integration –Typically, reduce a two-dimensional image into a one- dimensional dataset Normalization –Remove frame-to-frame variation to put them all onto the same scale Subtraction –Removing artifacts by subtracting background data from the sample data Averaging –Multiple noisy points can be averaged

29. Future work on the Processing pipeline Support more sciences (XPDF) Add branching, merging, and other non-linear flows Run calculations via HPC Passerelle workflows More, faster, better processing steps

30. Try DAWN for yourself! DAWN 1.7.1, available now! http://www.dawnsci.org See directions on how to use DAWNSci – “Getting started with DAWNSci” Videos on how to do use slicing, data reduction, Python scripting, processing at https://www.youtube.com/user/DAWNScience https://www.youtube.com/user/DAWNScience Follow us on Twitter - https://twitter.com/dawnsciencehttps://twitter.com/dawnscience Read the article about us in the Eclipse newsletter - https://www.eclipse.org/community/eclipse_newsletter/2015/j anuary/article3.php https://www.eclipse.org/community/eclipse_newsletter/2015/j anuary/article3.php DAWN paper accepted for publication, doi: 10.1107/S1600577515002283 Email us: scientificsoftware@diamond.ac.uk

31. +1 0 -1 Sign in: www.eclipsecon.org Evaluate the sessions