Monday, July 20, 2015

True random numbers

Generating random numbers is probably impossible. The substitute is generating pseudorandom (see a video here) numbers according to some deterministic rule well explained, for instance, in Knuth, (1997).  But the doubt that pseudorandom numbers is not enough usually sticks with you. So where having real random number, if they exist ?
You can try hardware generated random numbers. One particular set of these random numbers generators come from Dirk EddelBuettel who actually uses Mads Haar work for bringing true random numbers to R. Dirk points also to a nice introduction to random number generator, Maads Haar (1999), and an R package called random.


Dirk Eddelbuettel, random: An R package for true random numbers, 2006

Mads Haar, Introduction to random numbers (see also here), 1999

Knuth D.E. The Art of Computer Programming, Volume 2: Seminumerical Algorithms, Third Edition. Addison-Wesley, 1997. ISBN 0-201-89684-2. Chapter 3. [Extensive coverage of statistical tests for non-randomness.]

Friday, July 17, 2015

Site Specific Long Wave Radiation budgets

Estimating the longwave radiation is certainly a relevant task for any hydrologist who deals  with snow modelling and evapotranspiration (or, BTW, is trying to assess and close the whole hydrological budget).
This paper follows another one, that was written for the shortwave counterpart, which can be found here, and uses the same toolbox of components for calibration and other tasks (see figure below, for instance).  In order to obtain the results of the paper, a new JGrass-NewAGE component was implemented and tested and documented here.
The component and the related material performs a re-parametrization of ten empirical formulas found in literature, and introduces a regression to obtain the parameterizations coefficients in any location, based on those measured in Ameriflux site.

Information on the GEOFRAME site contains also indications for running the components code, and a working example of simulation.
The R script that contains the regression of parameterisations' coefficients be found on GIThub.
The published version of the paper is here.

Wednesday, July 15, 2015

Ecological Feedbacks of desertification: Stability and Resilience of Ecosystem and Society in arid Environments

This includes the outstanding presentation given by Paolo D'Odorico (GS) at the 2015 GII Ph.D. days. Besides the topic in itself, which is very interesting, it shows that hydrology is an inclusive science that moves toward the science of environment including all the processes and interactions. This lecture, however, deals with the global scale.

Monday, July 13, 2015


At the recent Ph.D. days I had a nice short talk with Katia Cugerone about disdrometers. Since she is pretty well informed I asked for some bibliography, and she promptly sent these references you will find below. She especially delighted me telling me about how in the Fourties researchers had studied the size of drops by collecting them in floor and absorbing paper.


About first methods of rain drops measure (with floor and absorbing paper) 

1) Laws, J. O. & Parsons, D. A., The relation of raindrop-size to intensity, Transactions, American Geophysical Union, 1943, 24, 452-460

2) Marshall, J.; Langille, R. & Palmer, W. M. K., Measurement of rainfall by radar, Journal of Meteorology, 1947, 4, 186-192

3) Marshall, J. S. & Palmer, W. M. The distribution of raindrops with size, Journal of Meteorology, 1948, 5, 165-166

Impact Disdrometer JWD (in German) 

4) Joss, J. & Waldvogel, A. Ein spectrograph fur Niederschlasgstropfen mit automatischer Auswertung (A spectrograph for the automatic analysis of raindrops) Pure Applied Geophysics, 1967, 68, 240-246

Optic Disdrometers (THIES and Parsivel, the most famous)

5) Frasson, R. P. M., L. K. Cunha, and W. K. Krajewski (2011), Assessment of the Thies optical disdrometer performance, Atmospheric Research, 101 (1), 237{255, doi: 10.1016/j.atmosres.2011.02.014.

Video-Disdrometers (the recent ones, more precise and costly)

6) Kruger, A. & Krajewski, W. F. Two-dimensional video disdrometer: A description, Journal of Atmospheric and Oceanic Technology, 2002, 19, 602-617

7) Schönhuber, M.; Lammer, G. & Randeu, W. One decade of imaging precipitation measurement by 2D-video-distrometer, Advances in Geosciences, Copernicus GmbH, 2007, 10, 85-90

A comparison between different disdrometers

8) Tokay, A.; Petersen, W. A.; Gatlin, P. & Wingo, M. Comparison of raindrop size distribution measurements by collocated disdrometers, Journal of Atmospheric and Oceanic Technology, Journal of Atmospheric and Oceanic Technology, American Meteorological Society, 2013, 30, 1672-1690

Sunday, July 12, 2015

Scientific Software's Myths

In preparing the work of the new Ph.D. student that will arrive this fall, I think a reading of there two posts "The myths of bioinformatics software" by Dr. Lior Pachter (GS) and the response by Dr. Titus Brown (GS) can help a lot. While I do not marry the negativist attitude of Patcher, I cannot deny that many of his statements are, in my experience, correct. I endorse more Brown's position, however.

I suggest that Ph.D. applicants look carefully both the positions (and the intricate series of links). For me, I certainly remain with GPL. At the same time,  I would warn the applicants that I am oscillating towards a thesis topic which would sound like "Design Patterns for Hydrology" (not forgetting, certainly what I wrote on GEOtop 3.0).

P.S. -I also totally endorse this Brown's statement: "From my few involvements with working on non-free software, I would also add that selling software is a tough business, and not one that automatically leads to any profits; there's a long tail, just as with everything else, and I long ago decided that my time is worth more to me than the expected income from selling software would be. (I would be thrilled if a student wanted to try to make money off of our work, but my academic work would remain open source.)".  I saw so many colleagues that believe they can sell their software or keep it close, failing miserably and missing the leadership they could have. I know also some remarkable exceptions though (Hydrus, Flo2D especially).

Friday, July 10, 2015

Water for life: the study of the network of interactions in the hydrological cycle and their effects

I wrote several time what I do. The following is the translation is the synthesis I prepared recently for high school students, hoping to fascinate them and drive them to the study of hydrology.  

My research consists in determining hydrological fluxes, from the sky to the earth, and again to the sky. In its flow, water sculpts earth surface, feeds life, sustains the ecosystems complexity, and is at the core of many economic activities.  The quantification of  water fluxes  is not trivial at all. It requires the use of sophisticated mathematics and implies a great variety of measures. By myself I make computer models. 

It would be a mistake to believe that the physical/mathematica details  of the hydrological cycle are known. All the hydrological cycle is ignited by sun’s radiation  which provides  the energy transformed in the hydrosphere in other forms and never trivially, by very complex dissipative structures.
Among  these: river networks, “lines” which cover (drain)  entire surfaces; vegetation, and plants which eat photons to fix carbon in their structures (from atmospheric C02) and produce oxygen  (from H20) using photosynthesis. My research focus in following water interactions through models.

With my collaborators, I developed two models: GEOtop and Jgrass-NewAGE.  
The first is a hyper-resolution model: it partitions a catchment with a grid cells of a few meters side and on this grid mathematically treats radiation, infiltration, evaporation, transpiration, rain and snow fall, snow metamorphism, soil freezing, and runoff production. All this complexity is not an end in itself, but is deemed necessary to understand local hydrological phenomena as soil moisture distribution, or shallow landslides triggering.
The second model instead tries to give answers at catchment scale, averaging out hydrological quantities, but without loosing the necessary and relevant information.  JGrass-NewAGE is used to understand what happens in medium rivers, as Adige, to large river basins, as Blue Nile: it also helps in understanding how hydrology affects and is affected by the climate crisis. 
Informatics has an important role in my research. JGrass-NewAGE,  more than a model is a modelling system, based on sophisticated informatics suitably developed to build environmental models and to make easier the interactions among researchers. 

Thursday, July 9, 2015

Paolo Benettin explaining his Ph.D thesis on travel time distributions and catchment hydrology

During the last days we had in Trento the GII 2015 Ph.D. days. Fourty two Italian students in water engineering and related topics gathered in Trento to show their work, and exchange ideas. Among them there were the three recently graduated that a GII committee selected as the best Italian thesis for the last year graduates, and among them, Paolo Benettin. Paolo (I was in the committee that approved his graduation) talked about: "Catchment transport and travel time distributions". In this thesis, besides developing some case studies he also tried to give  a  definitive arrangement to the theory of travel time distribution. The talk he gave is now on my youtube channel:

The presentation is also available on slideshare:

And finally his thesis can be downloaded from here:

Paolo Benettin, Catchment transport and travel time distributions: theoretical developments and applications, University of Padua, 2015

Use of this information requires proper acknowledgment of sources.

Sunday, July 5, 2015

Theory and Practice of Reproducible Research

In the occasion of the GII Ph.D. days, I am giving a talk about Research Reproducibility and Replicability. You can find my presentation on Slideshare, as usual. The slides below the figure are actually those of the talk I gave in Perugia October 12, 2016

The old presentation (which correspond to the youtube video, is here).

Please find the reference to tools and resources inside the slides. My talk is available trough my youtube channel:
Enjoy it!