The Story of Shadow and Orange

This is a long story. I remember when started my PhD in Italy. There I met a researcher and he said to me: »You should do some simulations on x-ray optics beamline.« »Yes, but how should I do that?« He gave me a big tape, it was 1986. I soon realized it was all code. But it was a code called Shadow.

I started to look at the code, to play with it, do some simulations… Soon my boss told me:

»You should do a simulation with asymmetric crystals for monochromators.«

»But asymmetric crystals are not foreseen in this code.«

»Yes, think about how to do it. You should contact Franco Cerrina, he’s the author of Shadow.«

I indeed contacted prof. Cerrina and at that time this was not easy, because there was no direct e-mail. What we had was called a digital deck net, Digital Computers Network. I had to go to another laboratory just to send him an e-mail. Soon, he replied: »Come to see me.« I managed to get some funding to go to the US and for the next two years I spent a good amount of time in Madison, Wisconsin.

I started to work with prof. Cerrina and it was thanks to my work on Shadow that I was called by the European Synchrotron Facility and they offered me a position. But soon I stopped working on Shadow, because I was getting busy with other things.

It was only in 2009 that I contacted prof. Cerrina again. We needed to upgrade our software, so I went back to the US two or three times and started working on what is now Shadow3.

 

In 2010 I organized a trip to go visit again with my family for the summer. We booked the house, we booked the trip… And it was ten days before the departure that I learned that Cerrina died. And since everything was already organized, we decided to visit the US anyway.

There, I went to Cerrina’s laboratory and met his PhD student, who was keeping his possessions. I said to her:

»Tell me everything you were doing recently and I will try to recover what I can.«

And at that moment, she said many things were on this big old Mac. So I proposed to buy this Mac from her, but my home institution wasn’t happy, they saw no reason to buy a second-hand Mac. Even though it contained some important things Cerrina was working on!

Luckily, I managed to get it and I was able to recover many things from it. Moreover, I kept maintaining the Shadow code, because it is a standard software in the community. At the very beginning, the source was not public. Then it was eventually published, but the code was very complicated and nobody managed to recompile that. Thus I decided to clean the code and finally we completed the new version of Shadow in 2011.

 

Three years ago it was time to update Shadow again, especially the interface. One day I discovered Orange and I thought ‘it looked nice’. In that exact time I met Luca [Rebuffi] in Trieste. He got so excited about Orange that his PhD project became redesigning Shadow’s interface with Orange! And now we have OASYS, which is an adaptation of Orange for optical physics. So I hope that in the future, we will have many more users and also many more developers helping us bring simple tools to the scientific community.

 

— Manuel Sanchez del Rio

Oasys: Orange Canvas applied to Optical Physics

This week we’re hosting experts in optical physics from Elettra Sincrotrone Trieste and European Synchrotron Radiation Facility in our laboratory. For a long time they have been interested in developing a user interface that integrates different simulation tools and data analysis software within one environment. It all came true with Orange Canvas and the OASYS system. We’ve already written about this two years ago, when the idea first came up. Now the actual software is ready and is being used by researchers for everyday analysis and prototyping.

 

OASYS is basically pure Orange Canvas (Orange but no data mining widgets) that is reconfigured for the needs of optical physicists. What our partners from Italy did (with the help of our lab), was bring optic simulation software used in synchrotron facilities into a single graphical user interface. What is especially incredible is that they managed to transform Orange into a simulation platform for building synchrotron beamlines.

 

In essence, researches in synchrotrons experiment with actual physical objects, such as mirrors and crystals of different shape and size to transmit photons from several light sources of the synchrotron to the experimental endstations. They measure a broad array of material properties through the interaction with the synchrotron light and are trying to simulate different experiment settings before actually building a real-life experiment in the synchrotron. And this is where OASYS truly shines.

beamline in synchrotron

beamline in synchrotron

Widgets in this case become parts of the simulation pipeline. Each widget has an input and output beam of light, just like real life devices, and the parameters within the widget are physical properties of a particular experimental object. Thus scientists can model the experiment in advance and do it much quicker and easier than before.

visualization of light properties

Furthermore, Orange and OASYS provide a user-friendly GUI that domain experts can quickly get used to. There are anecdotal evidences of renowned physicists, who preferred to do their analysis with outdated simulation tools. However, after using OASYS for just a few days, they were already completely comfortable and could reproduce previously calculated results in a software without any problem. Moreover, they did it within several days instead of weeks as before.

 

This is the power of visual programming – providing a user-friendly interface for automating complicated calculations and quick prototyping.