GSW2020 - Photos and material

You can see here some photos of the GEOframe Winter School 2020. The material and the final refine OMS/GEOframe GWS2020 project can be found on

• Zenodo: https://zenodo.org/record/3627007#.Xir75CN7nb0. 

It contains all the needed input and output files for executing the School's project. It will not work if you do not do all the right operation. Therefore, please browse the school material in order starting from the first post.

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GWS2020 - The Bonus II: Richards equation treated better better than in Hydrus 1D

The second bonus of the GEOframe Winter School on GEOframe is about the Richards' equation. Here we present the ongoing work by Niccolò Tubini (AboutHydrology) in his doctorate. In particular he is presenting how his code is working and why we believe it is a good code.

The presentation by Niccolò is divided into 2 parts: I and II.  The illustrated Jupyter Notebook as wells as the codes can be dowloaded from Github. There you can find also the Jupyter Notebooks and also browse the other software, including the Richards1D version coupled with the energy budget.

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GWS2020 - The Bonus I: A little on Travel Times

In the last days of the GEOframe WinterSchool 2020, most of the time was dedicated to simulating with the software but we also give a little clue on  topics that we could not expand more. This is the case of travel times modelling (and/or residence time).  Here Marialaura Bancheri (GS, Abouthydrology) talks a little about the theory and the applications she did mainly in her thesis.

You can watch the video of her talk here.  So far we did just the application that can be seen In Marialaura's thesis which are mostly demonstrative that real. Soon, however, in the project WATZON, we will use them massively.

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GWS2020 - Rainfall Runoff

Here we are introducing some modules for rainfall runoff modelling present in GEOframe.  We also maintain some material of the 2019 GEOframe Winter School that can be though interesting.

• The GEOframe type of models (YouTube2020)
• Representing the Hydrological Dynamical Systems (YouTube2020)
• The Embedded Reservoir Model (YouTube2020)
• The ERM sim file (Part I, II, III)
• The Net3 Graph
• LUCA calibration of the ERM
• Examples of Application
• The Posina Catchment (Abera et al., 2017a)(YouTube2019)
• The Blue Nile (Abera et al. 2017b) (YouTube2019)
• The Basilicata Civil Protection (YouTube2019)

• Net3 (YouTube2020)
• LUCA (YouTube2020)

Cavone River Exercise

• Part I (YouTube2020), Part II (YouTube2020), Part III (YouTube2020)

Goodness of fit notebooks

• Here

General references to Rainfall-Runoff

Beven, K. (2012), Ranfall Runoff, the primer, Wiley-Blackwell

Rigon, R., Bancheri, M., Formetta, G., & de Lavenne, A. (2015). The geomorphological unit hydrograph from a historical-critical perspective. Earth Surface Processes and Landforms, http://doi.org/10.1002/esp.3855

References besides the one already used

For seeing how to represent lumped hydrological models (you can give a look to this paper here)

Abera, W.W. (2016), Modelling water budget at a basin scale using JGrass-NewAge system. PhD thesis, University of Trento

Bancheri, Marialaura (2017) A flexible approach to the estimation of water budgets and its connection to the travel time theory. PhD thesis, University of Trento.


Bancheri, M., Serafin, F., & Rigon, R. (2019). The Representation of Hydrological Dynamical Systems Using Extended Petri Nets (EPN). Water Resources Research, 8(01), 159–27. http://doi.org/10.1029/2019WR025099

Bancheri, M., Rigon, R., & Manfreda, S. (2020). The GEOframe-NewAge Modelling System Applied in a Data Scarce Environment. Water, 12(1), 86–24. http://doi.org/10.3390/w12010086

Formetta, Giuseppe (2013) Hydrological modelling with components: the OMS3 NewAge-JGrass system. PhD thesis, University of Trento.

Formetta, G., Antonello, A., Franceschi, S., David, O., & Rigon, R. (2014). Hydrological modelling with components: A GIS-based open source framework, 55(C), 190–200. http://doi.org/10.1016/j.envsoft.2014.01.019

Patta, C, Costruzione di un modello idrologico di stima della disponibilità idrica in area pedemontana, Tesi di laurea (in Italian), Politecnico di Torino, 2018

For open questions about rainfall-runoff see also the Meledrio Posts.

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GWS2020 - Evaporation and Transpiration

Evapotranspiration accounts for most of fifty percent of the terrestrial hydrological cycle. We illustrate here some ways to estimate it with the tools offered by the GEOframe system. 

Radiation

We do not cover radiation in this school. We will just use it. For people interested, however, they can give a look to the material of 2019 School here.


The 2020 material

• Momentum and water vapor transport in atmosphere (YouTube2020)
• Evaporation as energy flow (YouTube2020)
• Derivation of the simplified energy budget (a là Penman-Monteith after Schymanski and Or) (YouTube2020)
• Simplified relatives of PMSO (YouTube2020)
• Leaf Temperature feedbacks
• Transpiration (YouTube2020)
• Further discussions on resistances and the physiology of plants in this video. 
• Evaporation from soil (YouTube2020)
• From leaves to canopies (YouTube2019 Video, YouTube2020)

The 2019 material

• Momentum and water vapor transport in atmosphere (YouTube2019)
• Penman-Monteith according to Shymanski and Or (PMSO- YouTube2019)
• PMSO with surfaces temperatures feedbacks (YouTube 2019)
• Evaporation from soil and Traspiration mechanisms (YouTube2019)
• From leaves to canopies (YouTube2019 Video)
• Documentation of GEOframe-NewAge component 2019
• Jupyter notebook with exercises
• Live YouTube video on the sim files and Jupyter notebooks

Out of schedule (for Chhay)

• Budyko curves derivation

Exercises

• You can follow this Jupyter notebook

References

Primarily for historic papers browse to the list by Dennis Baldocchi

• Haghighi, E., Shahraeeni, E., Lehmann, P., & Or, D. (2013). Evaporation rates across a convective air boundary layer are dominated by diffusion. Water Resources Research, 49(3), 1602–1610. http://doi.org/10.1002/wrcr.20166
• Lehmann, P., Assouline, S., & Or, D. (2008). Characteristic lengths affecting evaporative drying of porous media. Physical Review E, 77(5), 354–16. http://doi.org/10.1103/PhysRevE.77.056309
• Lehmann, P., & Or, D. (2013). Effect of wetness patchiness on evaporation dynamics from drying porous surfaces. Water Resources Research. http://doi.org/10.1002/2013WR013737
• Or, D., Lehmann, P., & Shahraeeni, E. (2013). Advances in soil evaporation Physics - A review. Vadose Zone Journal.
• Schymanski, S. J., & Or, D. (2017). Leaf-scale experiments reveal an important omission in the Penman–Monteith equation. Hydrology and Earth System Sciences, 21(2), 685–706. http://doi.org/10.5194/hess-21-685-2017
• Schymanski, S. J., Or, D., & Zwieniecki, M. (2013). Stomatal Control and Leaf Thermal and Hydraulic Capacitances under Rapid Environmental Fluctuations. PLoS ONE, 8(1), e54231–16. http://doi.org/10.1371/journal.pone.0054231
• Shokri, N., & Or, D. (2011). What determines drying rates at the onset of diffusion controlled stage-2 evaporation from porous media? Water Resources Research, 47(9), 584–8. http://doi.org/10.1029/2010WR010284
• Stroock, A. D., Pagay, V. V., Zwieniecki, M. A., & Michele Holbrook, N. (2014). The Physicochemical Hydrodynamics of Vascular Plants. Annual Rev. Fluid Mech., 46(1), 615–642. http://doi.org/10.1146/annurev-fluid-010313-141411

See also the discussions here:

• The vapour budget
• Soil-Plants fluxes
• Stomatal resistance and Evapotranspiration

And the mini-series: 

• The man who planted trees.

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The Jupyter notebooks and OMS project repository for the WSG2020

During the classes we use several Jupyter notebooks. You can find them at the appropriate OSF page:

Jupyter Notebooks

So if you search a notebook and you do not know where to find them: they are here.

The OMS project used is instead here:

Overall OMS3 project (available on Zenodo). It contains all the software used in the school.

GWS2020 - Interpolationg Hydro-meteorological data with Kriging

The third  day of the Winter School on the GEOframe system 2020 is about GEOframe are dedicated to interpolation by using Kriging and the use of Particle Swarm Calibrator.

• The Kriging's equations (YouTube2019 - Slides were a  little modified for 2020, YouTube2020)
• Variography (YouTube video 2019, YouTubeVideo2020)
• The GEOframe Spatial interpolation Package (SIK) (YouTube2019, YouTube2020)
• Error estimation (leave one out) within SIK (YouTube video 2019, YouTube2020)

Exercises 2020

• Jupyter notebooks
• Illustration of the.sim Files 
• Execute the experimental (semi)variogram (YouTube2019, YouTube2020)
• Fitting the theoretical (semi)variogram (YouTube2019 ,YouTube2020)
• Using the Particle swarm with SIK (YouTube2019 ,YouTube2020)
• The leave-one-out (YouTube2019 ,YouTube2020)
• Obtaining one single point estimate with Kriging in SIK (YouTube2019)
• Obtaining a raster of estimated with Kriging in SIK (YouTube2019)
• Again on .sim files (YouTube video 2019 )
• The Particle Swarm optimization. (YouTube 2020: part I, part II)
• Estimating the average variogram over a period of time (YouTube 2020: part I, part II, part III)
• Using Kriging (YouTube2020)
• Leave One Out (YouTube2020)
• Net3 (YouTube2020)
• Some Other Issues (Part I YouTube2020 , Part II YouTube2020)

Exercises 2019

• zip files containing Jupyter notebooks
• Illustration on the Jupyter Notebooks by Niccolò Tubini (Live YouTube video 2019)
• A little about parameter calibration (maybe with a little critical tone ?) (YouTube video 2019)

References

For general information about spatial interpolation of hydrological quantities, please see also "Rainfall and Temperature interpolation", on the AboutHydrology blog

• Marialaura Bancheri, Francesco Serafin, Michele Bottazzi, Wuletawu Abera, Giuseppe Formetta, and Riccardo Rigon, The design, deployment, and testing of kriging models in GEOframe with SIK-0.9.8, Geosci. Model Dev., 11, 2189–2207, 2018 https://doi.org/10.5194/gmd-11-2189-2018
• Andràs Bardossy, Introduction to Geostatistics, year unknown.
• Goovaerts, P. (1997). Geostatistics for Natural Resources Evaluation (pp. 1–488). New York : Oxford University Press.
• P.K. Kitanidis, Introduction to GEOstatistics, 1997 https://doi.org/10.1017/CBO9780511626166

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GWS2020 - Delineating catchments

The second day of the Winter School on GEOframe is dedicated to the watershed delineation and hillslope extraction. First the relevant concepts are given. Then GEOframe (Horton Machine) tools are used to get the desired results.

We recovered something from the first day.

• Hydrogeomorphology: the basic theory (YouTube video 2019,YouTube2020)
• OMS-Horton Machine tools description:
• Aspect
• Curvature
• Cutout
• Pitfiller
• Slope/Gradients
• TC or Topographic classes
• Hydrogeomorphology: the derived quantities (YouTube video 2019,YouTube2020)
• OMS-Horton Machine tools description:
• ExtractNetwork
• Flow Directions/Draindir
• MarkOutlet
• Water Outlet
• Hydrogeomorphology: extracting the hillslope (YouTube Video 2019,YouTube2020)
• Network ordering
• OMS-Horton Machine tools description:
• Network Attributes Builder
• A little on some geomorphic laws (YouTube video 2019, YouTube2020)
• Example: the Cavone case (Basilicata)
• Videos of the afternoon lab 
• Part I
• - (not very visible but understandable)
• Part II - (not very visible but understandable)
• Part III - (not very visible but understandable)
• Part IV - (not very visible but understandable)
• Part V 
• Part VI
• Part VII
• Part VIII 
• Again on using QGIS for dividing Cavone Catchment into subbasins (part I, part II, part II)
• The Horton Machine in gvSIG (not treated at the school but an interesting complement)
• Using QGIS for obtaining the centroids of subbasins  (YouTube video 2019)

References

• Various information from the AboutHydrology Blog
• Rigon, R., I. Rodriguez-Iturbe, A. Rinaldo, A. Maritan, A. Giacometti and D. Tarboton, On Hack’s law, Water Resources Research, 32(11), 3367, 1996
• R.Rigon, E. Ghesla, C. Tiso and A. Cozzini, The Horton Machine, pg. viii, 136, ISBN 10:88-8443-147-6, University of Trento, 2006
• W. Abera, A. Antonello, S. Franceschi, G. Formetta, R Rigon , "The uDig Spatial Toolbox for hydro-geomorphic analysis" in Geomorphological Techniques, v. 4, n. 1 (2014), p. 1-19

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GWS2020 - Getting Started with OMS and Jupyterlab

Day first of the Winter School on GEOframe was conceived to give people the taste of what OMS is and how to use it with Python lab. For the Installations, please refer to the Installation page. 

Not much information about Jupyterlab though. It will be given interactively using notebooks and explaining their contents.

• The philosophy behind OMS/GEOframe (YouTube video 2019, YouTube2020)
• The GEOframe deployment (YouTube2020)
• A brief introduction to the Object Modelling System (YouTube video 2019,YouTube2020, Also on VIMEO2020)
• OMS User Manual - Introduction (pdf, epub) 
• The OMS working environment (YouTube video 2020)
• OMS User Manual - The working Environment (pdf, epub)
• The structure of a .sim file (YouTube video 2019, YouTube2020)
• The existing manual excerpt (outdated but still useful) (pdf, epub)
• The OMS console (YouTube2020)
• Examples 2020.
• Examples 2019 (All the material in the .zip files. Notebooks in /docs folder)
• ex_00 (zip files)
• Examples-basic (zip files). Please find Jupyter notebook shown in video below in the doc directory of the zipped files.
• Example 001 (YouTube video 2019)
• Controlling Iteration (Ex 05) YouTube video 2019.
• Going on with examples: Again on You Tube Video Iteration, Bulk connect, Feedbacks
• Exercises 1&2
• Watertank  Example (zip files). Documentation in the doc folder.
• Water Tank example - Part I YouTube video 2019
• Exercises 3&4
• Creating a notebook from the scratch (Live YouTube video 2019 by Niccolò Tubini)

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Installing Java and OMS

The Winter School on the GEOframe system is approaching.  In this post you will find all the preparatory material of the school indexed.

Installations

You are not assumed to know Python or Java to participate to the School. However programs GOFRAME programs runs on Java 8. Input/Output of models will be treated by using some scripting in Python. We will communicate the appropriate notions during the classes but the interested can finfd plenty of courses on the web (for instance this comes from SciPy 2018. Other from SciPy here.)

• Java. GEOframe and OMS are written in Java and they require to have installed Java on your computer. Here you can find instructions to install Java on your computer.  OMS need Java 8 JDK.  Please note that you need the Java Development Toolkit (JDK) installed not the Java Runtime Environment (JRE).  You can watch several videos for Windows here but Windows user can follow our previous blogpost.  For Macs, look at here. Googling you can get more videos and information. 
• OMS v 3 Console. It is possible to use Docker to execute the programs but, after the experience of the last year with Docker installations on Windows, we preferred to use directly the Console. The OMS system installation traditional information can be found here: https://alm.engr.colostate.edu/cb/wiki/16961 and https://alm.engr.colostate.edu/cb/wiki/17107.  During the School we will use the Console 3.6.28. To install the Console, you have to download and unzip it, put it in a directory (folder) of your choice.  A new directory called oms-3.6.28-console will be created, inside of which you'll see:

• To start the Console from Windows, just click on the .bat file
• To start the Console from Mac OSX or Linux, open a Terminal and execute:
• % ./console.sh &
• The "&" just free the command line back and gives it back to you. 

• During the School we will use Jupyter and Python 3 for data management and visualisation. It would be great if you could arrive with Jupyter installed.
• The post at this link contains all the information needed. For installation of the software, we suggest Anaconda. For any problem contact us through the mailing list https://groups.google.com/forum/#!forum/geoframe-winter-schools. 
• To understand what a Jupyter notebook is about, please see its manual. However, we will use Jupyterlab.  (You can see a YouTube video about here).  One can think that Jupyter was heavily based on the look-and-feel of Mathematica notebooks: but Jupyterlab is a step ahead to something different. Installing Anaconda, you also have already installed Jupyter notebook. You can open Jupyter lab by the Anaconda Console, or issuing the command  Jupyter lab at a terminal (called DOS prompt in Windows).

• The manual of Jupyterlab is here.
• BTW, it will be useful to have also a GIS of your choice installed. We suggest QGIS.

Set the Java Home in the Console

• Just open the pull-down menù below from the first Console Window  (you must just click on the plus sign on the fourth icon on top left) and then insert in the Java Home the full path of your Java Home (if you do not know where it is, look at here: MS Windows, Mac/Linux)

New: The OMS project and software used during the school is here on Zenodo. Download it for using it later according to the what you will find on the next pages.

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How to check Java and Java home on Macs

To understand which Java you have

• Open Terminal.
• First confirm you have JDK by typing “which java”. It should show something like /usr/bin/java.
• Check you have the needed version of Java, by typing “java -version”. 
• If you do not have Java JDK, install it. Please the Java Development Kit. Not the Java Runtime Environment (JRE). To get use either the adoptJDK site or the Zulu site. For the present GEOframe system, the JDK 8 is necessary (Geotools do not work with Java 9 or more). Reasons why Oracle sites are not preferable are well documented here.

To set Java Home

• JAVA_HOME is essentially the full path of the directory that contains a sub-directory named bin which in turn contains the java.
• For knowing where it is, at the terminal prompt issue the command: %/usr/libexec/java_home -V
• If you installed the adoptJDK, your directory should be something — /Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home

Setting JAVA_HOME for use of Java from Terminal

• Set JAVA_HOME using this command in Terminal:  export JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-8.jdk/Contents/Home
• Finally issue: echo $JAVA_HOME on Terminal to confirm the path

You should now be able to run your applications from the terminal