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Re-formatting tables with astropy

The fact that astropy is a very powerful tool is certainly well known these days, but I would like to briefly express my admiration especially for the Table package. This package allows, among many other things, to quickly convert tables between various formats (ASCII, CSV, LaTeX, many others) and it also allows to re-format individual columns. For example, if you would like to change the number of significant digits for a specific column (“seeing”), you simply open the table and assign the usual format specifier to this column like this:

from astropy.io import ascii




The situation of researchers

Apart from research itself, I am also interested in the situation of researchers. Actually this has caught my interest since realizing sometime in the middle of the first year of my Ph.D. that competition for scientific positions is extremely high and that it is therefore crucial for science workers to join forces if we want to ensure some minimum standards.

PhDnet survey 2009During that time I actively started to participate in the Max Planck PhDnet, the association of Ph.D. candidates in the Max Planck Society, and in 2009 became their spokesperson. One of the largest projects we performed during that time was to conduct a survey among all Ph.D. candidates about their working conditions. With a ca. 50% participation rate, this was the first large and representative Ph.D. candidate survey in the Max Planck Society.


The survey report (direct link to PDF download) has been distributed (by the Max Planck Society) to all directors and we have received quite some press coverage during that time. One of the spicy findings was that there was no difference in working conditions of contract holders and stipend holders, thereby questioning the different payment modalities. It took several more years (and some dirty fights), but eventually in 2015, the Max Planck Society decided to get rid of stipends. For the full story, see the Science Careers article “Junior Max Planck researchers win reforms“.

For most researchers it comes without asking that you want to shape your own working environment towards the better. However, sometimes junior researchers have to face strict opposition when being concerned about their careers, their contracts or such. Often it is then said that (junior) researchers should “focus on their research” and not “waste their time” with political actions. This is, with all due respect, nonsense. If it’s not for us — the junior researchers — to ask for better employment contracts, career perspectives and fair treatment in applications, then who is going to lobby for us? Ah, and sometimes it is also at least indirectly suggested that only dimwits are concerned about their careers and contracts. The really excellent scientists don’t need to worry, it goes. Let me ask my friend Albert to answer this: “I consider it important, indeed urgently necessary, for intellectual workers to get together, both to protect their own economic status and also, generally speaking, to secure their influence in the political field.” (A. Einstein, 1950. Out of my later years. New York, NY: Philosophical Library.) — a quote that I read in an excellent article about why junior researchers need to unionize.

15 April 2020 – This text used to be a part of my main website, but I will make space in my navigation bar for another topic that I deem more relevant these days: the climate crisis.

METIS in 500 words

METIS is the “Mid-Infrared ELT Imager and Spectrograph” and I will explain it by dissecting the complicated name:

Mid-infrared” refers to wavelengths between 3-20 micrometers. This range is also referred to as thermal radiation because things that are at room temperature emit the most light in these wavelengths. By looking at this wavelength range we can see objects in space that are at this temperature, about 300 degrees above absolute zero. These are, for example, planets that resemble the Earth, so not those hot Jupiter-like planets (that we have known for thirty years or so), but planets that may have an earth-like atmosphere and perhaps, yes… maybe even have a form of life. There is good hope that we’ll find an Earth-like planet in orbit around our closest star: Alpha Centauri. It is so bright that we have to be very careful when we observe it with METIS, otherwise our sensitive camera will be damaged. And that is exactly the challenge: block as much light as possible from the bright star until we can find the small planet nearby.

That is certainly the most spectacular use of METIS, but it is also the most risky one. Fortunately, there are many other things we can study with METIS. In our galaxy, the Milky Way, we will also make observations of the disks around young stars and the atmospheres of old stars. And in certain other galaxies we can also make observations in the mid-infrared light. In almost every galaxy there is a super-massive black hole in the center. And when that actively accretes matter, the surrounding swirl of gas and dust gets hot and at certain places it reaches room temperature so that we can easily see it in the middle infrared.

ELT” stands for “European Extremely Large Telescope” and that is the name of the largest telescope in the world that is now under construction. It is being built by a European organisation (the European Southern Observatory or ESO) on a mountain in the Atacama desert in Chile and will be ready in the mid 2020s. With its diameter of almost 40m, the area of that telescope will be larger than the areas of all current large telescopes combined! There is no company in the world that can produce such a large mirror and so the main mirror (the one that will be almost 40m in size) consists of 798 segments, each with a diameter of about 1.45m. And they all have to be placed in such a way that the whole mirror then becomes a parabola. Almost impossible, right?

Finally, “Imager and Spectrograph” refers to what the instrument will be able to do: record pictures and spectra. With the “Imager” we can for example take a real picture of an earth-like planet and with the “Spectrograph” we can analyze the light of that planet and compare it with models of atmospheres to discover what happens on that planet.

METIS — uitgelegd in het Nederlands



METIS is de “Mid-Infrared ELT Imager and Spectrograph” en we zullen deze ingewikkelde naam even uitleggen.


“Mid-infrared” betekent een bereik van golflengten (3-20 micrometer) die we ook thermische straling noemen omdat spullen die op kamertemperatuur zijn het meeste licht in deze golflengten uitstralen. Dus kunnen we op deze manier ook in de ruimte voorwerpen zien die op deze temperatuur, zo’n 300 graden boven het absolute nulpunt, zijn. Dat zijn bijvoorbeeld planeten die op de aarde lijken, dus niet die hete Jupiter-achtige planeten (die we nu al sinds dertig jaar of zo kennen), maar planeten die mogelijk een aard-achtige atmosfeer hebben en misschien, ja… misschien zelfs een vorm van leven kunnen hebben. Er is goed hoop dat we een aard-achtige planeet in orbit rondom onze nabijste ster zullen vinden: Alpha Centauri. Die is zo helder dat we erg voorzichtig moeten zijn als we die met METIS zullen waarnemen, want anders raakt onze gevoelige camera beschadigd. En dat is dan ook precies de uitdaging: zo veel mogelijk licht van de heldere ster blokkeren totdat we de kleine planeet in zijn buurt kunnen vinden.


Dat is zeker de spectaculairste bedoeling van METIS, maar ook de riskantste. Gelukkig zijn er nog heel wat andere dingen die we met METIS kunnen bestuderen. In ons sterrenstelsel, de Melkweg, zullen we ook waarnemingen doen van de schijven rondom jonge sterren en de atmosferen van oude sterren. En ook in bepaalde andere sterrenstelsels kunnen we in het midden-infrarode licht waarnemingen doen. In bijna ieder sterrenstelsel zit er namelijk een super-massaal zwart gat in het midden. En als dat actief materie aanzuigt, wordt die heet en komt op bepaalde plekken juist op kamertemperatuur zodat we ze dan makkelijk kunnen zien in het midden infrarood.


“ELT” staat voor “European Extremely Large Telescope” en dat is de naam van de nu in aanbouw zijnde grootste telescoop der wereld. Die wordt door een Europese organisatie (de European Southern Observatory of ESO) op een berg in de Atacama woestijn in Chili gebouwd en zal in 2024 klaar zijn. Met z’n doorsnee van bijna 40m wordt de oppervlakte van die telescoop groter dan de oppervlakten van alle huidige grote telescopen gecombineerd! Er is geen bedrijf in de wereld dat een zo grote spiegel kan produceren en dus bestaat de hoofdspiegel (degene die bijna 40m groot zal zijn) uit 798 segmenten, ieder met z’n 1,45m doorsnee. En die moeten allemaal precies zo geplaatst worden dat de hele spiegel dan een parabola wordt. Bijna onmogelijk, toch?


“Imager and Spectrograph” betekent wat we met de camera (METIS) zullen doen: plaatjes en spectra opnemen. Met de “Imager” kunnen we bijvoorbeeld een echt plaatje van een aardachtige planeet opnemen en met de “Spectrograph” kunnen we het licht van die planeet dan analyseren en vergelijken met modellen van atmosferen om te ontdekken wat er op die planeet gebeurt.

How to set up your Mac as a shared drive for TimeMachine on macOS High Sierra

I used to use my late 2014 Mac mini at home with an external hard drive connected as a shared drive to backup several Macs using TimeMachine. This has worked well for years now, but recently the clients stopped to recognise the Mac mini as TimeMachine server. I followed these two instructions and now it works:

  1. The official Apple support post to set up your Mac as a TimeMachine server (essentially: right click on the shared drive in the Sharing preference pane and select it to serve as a TimeMachine disk). This made the disk appear again in the client’s TimeMachine preference pane, but it wouldn’t allow me to connect saying (translating from German) “You don’t have the required permissions to use this disk”. Only after following the next step, did it work.
  2. This user-contributed instruction on the Apple discussions forum (essentially: create a folder on the shared disk and share the folder rather than the whole disk)

Don’t bother with all the old tips on the web saying that you need to download the ca. 30 € Apple server software. It doesn’t support TimeMachine anymore for newer macOS versions and it is not required anyway, as you can also just make it work using the built-in sharing feature.

The open science workshop at the Stifterverband

This is a follow-up to my post 2 days ago about open-ness in astronomy, with some observations and comments from the corresponding workshop yesterday in Berlin, organized by the Stifterverband. The workshop was visited by about 30 people from all parts of society — researchers, library managers, civil servants from national and foreign science ministries, as well as people from industry (software, automotive, airport services, among others). In the spirit of open-ness the workshop adopted the “Chatham House rule” which essentially says that you may report freely about what has been said, but only if individual participants cannot be identified.

The workshop was organised in discussions within the respective sectors science, administration and industry and round-the-table discussions with everyone. As always in a workshop with such a diverse audience and broad aim (“to explore potentials and challenges from open research and innovation processes”), it is hard to give a one paragraph summary of the many topics discussed, but I will try nevertheless.

An “innovation culture” needs to admit errors

Most participants agreed that open-ness is a mindset that helps with innovative thinking, but it was also agreed that there are limits to open-ness, e.g. due to privacy (e.g. patient data in medical applications) or security (e.g. when in connection with critical infrastructure) concerns. To be able to openly discuss not just final results, but also your way there (e.g. your methods), requires some tolerance towards failure. If you cannot risk to fail, you can also not be open as you will only talk about your project after you have achieved some major success. And it also requires some trust or self-confidence that you will have another good idea in case the one you publish today is being picked up by someone else.

The measure becomes the target

In the discussion group on open-ness in science the discussion was focused on the question “how can we fix science?”. Science is becoming more and more an industrial machinery, optimised for maximum impact and citation numbers, opting for certain results (that are often boring) rather than trying out radical new experiments (that often fail). Science managers and politicians try to increase the “output” for a given level of (public) funding and need to be able to measure the output in order to report on changes. Generally the output is now seen as number of papers and number of citations each paper receives. However, focusing too intensively on these narrow indicators leads to the effect that many scientists now try to maximise their impact as measured by these numbers, rather than try to work on something bigger that does not (immediately) result in a large number of papers or citations. Think about the gravitational wave experiments which produced null-results for decades – before receiving the Nobel Prize this year. Other metrics, such as Altmetic which measures the impact of your research in society, may be helpful to get a wider view of the relevance of research projects.

Publication bias

Typically people only publish their studies if they find a result. If nothing could be measured or the result was deemed not of interest, it is not published. A participant called the so-accumulated knowledge “dark knowledge” and cited an Austrian funding agency which estimated (by looking at allocated budgets) that this “dark knowledge” grows 2-3 times as fast as published knowledge. It was agreed that also failures should be published, but it was also agreed that publishing null-results is not honoured in our current research system, or as one participant put it: “How many unsuccessful scientists do you know”?

Science as the stroke of a genius or regular work?

Underlying many discussions about how to measure success in scientists, how to evaluate scientific work (and scientists themselves!), is the question of how scientific progress is perceived. Unfortunately many people still believe science progress when some genius has a fantastic idea. This can occasionally be the case, but usually even the genius bases his or her insight on published literature which to the most part consists of hard work by hard working people, trying out new methods and slowly progressing in understanding some topic. It was felt that this work is often not properly appreciated. We concentrate too much on people who have done some fantastic new thing, rather than on the many “smaller” scientists who contributed to the success of the “genius”. This is also reflected in the current job situation, especially in Germany, where there is little room for normal working academics: You’re either a (perceived) genius and can then advance to become a professor or you’re continuously on short-term “postdoc” contracts without stability or job security.


There was some uncertainty as to how best open up the scientific process to the general public. Some believed that the next big step, after simple press releases and more interactive talks / blogs / social media is a full participation of the general public via citizen science projects. Others were more cautious and thought this is just a “hype” that is only applicable to a small set of projects. Indeed in astronomy, the GalaxyZoo project mentioned also in my previous post was highly successful, but it is unclear if citizens’ help in classifying galaxies will be needed in the future given recent advances in machine learning codes.

What can science contribute to society?

Finally the question was discussed what can science contribute to the wider society? Here I’d like to describe two of the most widely discussed points:

  • Science contributes skeptical thinking. Skepticism is one of the basic traits of a good scientist and encourages everyone not to take claims for granted, but to critically ponder whether they can be true, ask for references, proof and repetition. In times of “fake news”, “climate deniers” and vaccination hoaxers, the importance of this trait cannot be overestimated. It was also stated that science needs to be healthy to encourage skepticism. If we only try to reach the maximal numbers of papers or citations, this does not necessarily help to question existing paradigms and make real progress.
  • Science may also contribute tools and best practices for open-ness, such as the distributed version-control system github, open access publication platforms, and other tools to openly share information. Note that also the world-wide web was initiated from a research environment (the CERN) and it was created in an effort to make information accessible. Nowadays, this would perhaps also be called open science…

Update (16 March 2018): The Stifterverband has published a white paper on Open Science at their webpage describing their initiative for Open Science and Innovation (both are in German).

Astronomy as an example for an open science

When a former Max Planck colleague who now works at the Stifterverband, a public-private think-tank, called me in October and asked if I wanted to take part in a workshop about open science, I was unsure what astronomy could offer in this regard. However, when simply writing up the tools and processes many astronomers use (and take for granted), it quickly becomes clear that astronomy is very much an open science already.

In the spirit of open science, I would like to document here my preparation for the discussion section of the workshop tomorrow.

What does openness in astronomy mean?

  • Open data: access to raw data (e.g. through the ESO archive) as well as access to surveys (e.g. through VizieR) and meta-data (e.g. through Simbad). The access is available for everyone and in most cases either in near real-time or after a proprietary period of maximum 12 months (in most cases).
  • Open source: access to scripts, libraries, programming tools, codes, … that are used to analyse the raw data and derive scientific results. In the most open projects (such as astropy), even the development process is open and anyone can contribute via e.g. github. Platforms such the Astrophysics Source Code Library, on the other hand, publish the final code itself and make it searchable through standard literature search engines.
  • Open access means free and unimpeded access to consolidated scientific results as published in peer-reviewed journals. While many relevant astronomical journals, including the just recently launched Nature Astronomy, are not open access by themselves, most (all relevant?) journals now allow publishing the author’s copy on preprint servers such as on the arXiv. Most current research articles can be found on “astro-ph” (the astrophysics’ section of the arXiv). Still troublesome, however, are technical articles (e.g. about telescope or instrumentation projects), that are published in the SPIE proceedings. A google search for the fulltext of the article, including “filetype:pdf” as a further filter, often reveals the author’s copy, however. In some cases, authors can “rebel” against the copyright notice they typically have to sign in order to publish an article (see example below for one of the articles published during my Ph.D.).


Example of a modified copyright agreement granting only a non-exclusive license to the publisher and thus allowing to publish my own article on my homepage or on preprint servers.

  • Apart from open data, open source and open access, open science can also encompass outreach and communicating with the public. This can be in more traditional “teaching” ways through blogs (e.g. the German SciLogs platform on which I have blogged about my trips to Chile during my Ph.D. and later), talks, open house days etc., but in some cases it can also mean directly embedding citizens in your research project, such as demonstrated successfully by the GalaxyZoo project that involves citizens to classify galaxy morphologies, a task in which humans have so far been better than machines.
  • Open science should can also include transparent selection procedures. After all, the particular selection of proposals, job candidates, laureates etc. can shape the de-facto view of a field for a long time and therefore comes with big influence and power. This could, for example, mean to publish the criteria which will be used to select a candidate for a job and to democratically nominate committees that decide about proposals and prizes. This is partly the case in astronomy, e.g. the committees that help select proposals for the Deutsche Forschungsgemeinschaft are elected by the scientific staff themselves.
  • Last, but not least, I believe open science should also include democratic structures in universities and research institutes. Usually, in German universities, there are “Fachschaften” that have a say on the selection of professors, and the Max Planck society sponsors one of the largest Ph.D. networks in the country, the Max Planck PhDnet. On the more senior, but not yet tenured, level, however, the situation is less good. Attempts to form a postdoc network within the Max Planck Society have not been greeted with sympathy in several institutes as some directors fear to lose influence if juniors also have a say. This is, however, not specific to astronomy, but rather a general symptom of the research and higher education landscape in Germany.

Why do we promote open-ness in astronomy?

Astronomy is a highly competitive field (typically only one out of 20 astronomy Ph.D.s eventually gets a tenured research position). Open-ness in astronomy would not be supported if it weren’t also promoting competitiveness and productivity.

  • Regarding data, observatories, that run big telescopes, promote open science in order to increase the observers’ desire to quickly publish “their” data (lest others “steal” them). Top-nodge data are often publicly available from the start. The first observations with the next, biggest space telescope will be open access from day 1, as announced today. The first observations for instruments built for the European Southern Observatory ESO, are also usually publicly available from the start, e.g. these GRAVITY science verification data. Other data are usually openly accessible after a 12 month “proprietary period”. This can sometimes be in conflict with the “owners” (PIs) of the data.
  • Regarding open source, the motivation to publish tools and software code is manifold: the author(s) of the code publish it in order to promote their code (and collect citations to associated research papers), but also so that others can contribute in the development. Last but not least, publication is the best way to help others in finding bugs and errors and therefore make your own research more credible.
  • Open access is in the interest of everyone except scrupulous publishers who want to make a profit from publicly financed research. It helps to promote science and the scientific method, also in the wider society, if the basic results are openly accessible. And it helps researchers from poorer countries who cannot afford paying expensive subscription fees to Nature, Science et al.
  • Public outreach also helps everyone, but can be a burden for researchers who also have to teach / supervise students, manage projects, deal with bureaucracy and publish, publish, publish. Motivations to nevertheless indulge in public outreach reach from simple PR for your own research (in order to attract more research money or to boost one’s ego…), but can also include serious collaboration with the public (see GalaxyZoo). Often the motivation for being active in public outreach is also to promote the scientific method (e.g. the Science March initiatives) or a feeling of a moral obligation as publicly funded research should also be of benefit for the public.
  • Transparent selection procedures and democratic structures, finally, are also a win-win situation: researchers gain trust in the process and will therefore try harder to win prizes, fellowships and jobs. The academic institutions, on the other hand, win by becoming more attractive to a wider range of (international) applicants. The only downside is an increased effort of documentation / communication, but I believe the benefits well outweigh the costs.

I am interested to see the discussion tomorrow and will try to report back with a view from the other participants / fields as well!

Update 15 Nov:

Een verhaal over mij, de sterren en ons, en mijn werk

Een verhaal over mij, de sterren en ons, en mijn werk

voor de Nacht van de Nacht, 28 oktober 2017, Panbos Katwijk

Hallo, ik ben Leo en kom origineel uit Oostenrijk maar heb lange tijd in Duitsland gewoont. Vier maanden geleden ben ik met mijn gezin, mijn vrouw en onze drie kinderen, naar Leiden verhuisd. Ik werk aan de Sterrwacht van de Universiteit Leiden en wil jullie vandaag graag wat vertellen over de sterren en ons..

Overdag, wanneer het helder is, zijn we bezig met ons werk, overleggen met collega’s, praten met vrienden en gezinsleden. We kunnen dan snel vergeten dat er nog veel meer om ons heen is! Indien de nacht helder was, zullen we vandaag de maan kunnen zien. Hij heeft een afstand van rond 380.000 km — tien keer de hele wereld rond! En toch is deze afstand klein in vergelijking met andere astronomische objecten. Dus gebruiken astronomen niet kilometers om de afstand te beschrijven maar de snelheid van licht. En die is heel snel! Het heeft maar rond één seconde nodig om van de maan naar ons te komen. Dus is het makkelijk om ook verdere afstanden te beschrijven. Bijvoorbeeld: onze zon is ongeveer acht licht minuten ver en de (kleine)planeet Pluto slechts vijf en half uur. [Kennen jullie die?] De andere planeten zijn niet zo ver en er zijn er acht in totaal: Mercurius, Venus, de aarde (onze wereld), Mars, Jupiter, Saturnus, Uranus en Neptunus.

En er is nog veel meer: We wonen maar op één planeet van miljarden in ons sterrenstelsel, de Melkweg! Er zijn rond 200 miljard sterren in de Melkweg (die we bij heldere hemel en indien het heel donker is, kunnen zien) en elke ster kan enkele planeten hebben! Tot vandaag zijn er rond 3700 planeten buiten ons zonnestelsel bekend, maar we weten al dat er nog veel meer planeten moeten zijn omdat we tegenwoordig alleen de grootste en bizarste planeten kunnen waarnemen!

In Leiden bouwen wij dus een camera voor de volgende, grootste telescoop van de wereld, de European Extremely Large Telescope. Hun spiegel is groter dan alle spiegels van de huidige telescopen samen! En met de camera die we bouwen (die heet METIS) kunnen we dan voor de eerste keer planeten die op de aarde lijken bestuderen en misschien een andere planeet vinden waar leven mogelijk is. Maar tot dit moment is de aarde de enige planeet in het zonnestelsel en ook in de hele Melkweg, die we kennen en waar leven mogelijk is. Dus moeten we haar goed beschermen!

What I did the last 2.5 years…

After working on GRAVITY for about three years, I continued my postdoc phase at MPE 2015/2016 with a self-funded (*) project. (*) “self-funded” is of course a very misleading term as I didn’t fund myself out of my pocket (but was rather funded by generous German tax money via the Deutsche Forschungsgemeinschaft DFG). This project is not completely finished, but my family and I moved to Leiden this year so that I could take on my current position as “calibration scientist” with E-ELT/METIS at the Sterrewacht of the University of Leiden. I hope to complete this project with the next year or two, however, with the help of a recently recruited Ph.D. student. In the meantime, the DFG has asked everyone who was funded in this “priority programme” on the interstellar medium to write a report about what they did. This was actually an interesting reflection on the last 2.5 years of research and I would like to share it here (PDF) with anyone who would like to read it.

Ph.D. project: The multi-wavelength view of the AGN – star formation relation

I am happy to announce a new position to work on a Ph.D. project at the Sterrewacht Leiden / Leiden University

The multi-wavelength view of the AGN – star formation relation

One of the long-standing questions in astrophysical research is what exactly triggers the onset of Active Galactic Nuclei (AGNs). The aim of this project is (1) to study the nuclear star formation history in a well selected sample of nearby AGNs with exquisite data (VLT/X-SHOOTER spectra) and (2) to participate or lead pioneering efforts to study gas, dust and star formation in the parsec-scale environment of nearby actively accreting super-massive black holes using the upcoming infrared interferometer MATISSE on the VLTI.

Supervisors: Dr. Leonard Burtscher, Prof. Dr. Walter Jaffe

Promoter: Prof. Dr. Bernhard Brandl

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