November 10, 2020

How to set a multiuser Jupyterlab server with Jupyterhub (in Windows with Docker)

November 10, 2020/ Saul Montoya

When teaching or working with Python there is a challenge to have and work simultaneously with the same Python version and Python packages. Jupyterhub is a great solution to bring notebooks to a group of users with admin tools and many more features. We have done a tutorial to install Jupyterhub with Jupyterlab in a local lan or wifi network. The tutorial shows the procedure to run Jupyterhub from Docker in Windows, set up a native authenticator and configure an admin and users.

November 04, 2020

How to do a simulated groundwater head difference map in MODFLOW and ModelMuse - Tutorial

November 04, 2020/ Saul Montoya

This is a tutorial about some functionalities of Model Muse to analyze and process layer heads or parameters. The applied example was done based on a previous tutorial of a model with 3 stress periods, one static and two transient periods of 10 days. The simulated map shows the head difference in the last 10 days.

November 03, 2020

How to clip polygon layers with Python, Fiona and Shapely - Tutorial

November 03, 2020/ Saul Montoya

This tutorial shows the entire procedure to clip a polygon layer to an area of interest in Python with the use of spatial libraries as Fiona and Shapely. The tutorial opens the polygon and clip layer as fiona elements, interpret the geometries as shapely Polygon datatypes, clip the polygons and store results as an output shapefile with the corresponding metadata.

October 30, 2020

Review of the latest functionalities of the new release of MODFLOW 6 (mf6.2.0)

October 30, 2020/ Saul Montoya

Modflow6 is the latest version of the USGS code for groundwater modeling MODFLOW. This version has been coupled with another USGS open source software as Model Muse and Flopy and can implement diverse spatial discretization structures on a complete rearrangement of packages and keywords. We feel that there is a gap on the capabilities from a common groundwater modeler to adopt all the new development on Modflow and other open source groundwater software therefore we have prepared a video with the summary of this new release.

October 26, 2020

How to clip Sentinel 2 bands to an area of interest with Python, Rasterio and Fiona - Tutorial

October 26, 2020/ Saul Montoya

Under the concept of “Python spatial” we have developed a tutorial for the spatial processing of multiple bands from a Sentinel 2 image. The tutorial shows the procedure to read the set of bands, import a shapefile, clip each band and export the clipped version in another folder. The spatial process is independent from raster resolution and can be easily modified for Landsat images.

October 21, 2020

How to set a Multi Aquifer Well (MAW) in MODFLOW 6 and Model Muse - Tutorial

October 21, 2020/ Saul Montoya

Modeling the dynamic of the groundwater flow related to pumping was a challenge with the traditional Wel package in MODFLOW since wells are screened on the most part of the well depth crossing multiple layers of a groundwater flow model. The Multi Aquifer Well (MAW) package came as a solution for this complex behaviour of layer interaction in Modflow. Model Muse with Modflow6 can implement the MAW package with ease.

This tutorial shows the complete procedure to set up a MAW well on a 3 layer groundwater flow model, gives an overview of the package options and represents the well heads and well rates with scripts in Flopy.

October 16, 2020

Geospatial triangular interpolation with Python, Scipy, Geopandas and Rasterio - Tutorial

October 16, 2020/ Saul Montoya

Under the concept of “applied geospatial Python” we have developed some procedures / tutorials of some common spatial analysis tasks done on desktop GIS software. The aim isn’t to reinvent the wheel but to explore the current Python tools and libraries that can create, analyze and represent both vector and raster spatial data.

Triangular interpolation is one of several types of interpolation techniques available in both Python and GIS software, however the advantage of working with Python is that the interpolation is a function where you can get the interpolated value on a specific point while in GIS software you are required to create a raster and sample values from the raster (.. as far as we know).

We have created a tutorial with a complete procedure in Python to import points with elevation as a attribute, creates a triangular interpolation function and has two spatial outputs: an interpolated geospatial raster in TIFF format and a shapefile with elevation attribute for another set of points. The tutorial uses several Python libraries as Matplotlib, Rasterio, Geopandas, Scipy.

October 08, 2020

Geospatial crop counting from drone orthophotos with Python, Scikit Learn and Scikit Image

October 08, 2020/ Saul Montoya

Orthophoto from drones provide us aerial imagery with spatial resolution in the scale of centimeters. With this high definition and cheap ortophotos we can interpret, analyze and quantify objects on a horizontal distribution by means of machine learning libraries for image recognition and cluster analysis. We have done an applied example of plant recognition and counting from a drone orthophoto with Python and the machine learning libraries Scikit Learn and Scikit Image. The whole process is geospatial, as it works with raster and shapefiles and results are finally displayed on QGIS.

October 02, 2020

Basic tutorial of geological modeling with Python and Gempy

October 02, 2020/ Saul Montoya

Gempy is an open-source library for modeling geology written in Python. The library is capable of creating complex 3D geological models including structures, fault networks, and unconformities and it can be coupled with uncertainty analysis.

We have created a tutorial of geological modeling based on geological contacts and surface orientations. The tutorial was developed in a Gempy container that runs under Docker in Windows 10; the tutorial covers the software installation and the geological modeling scripting.

September 30, 2020

A comprehensive list of specific Python packages for hydrogeology and groundwater modeling

September 30, 2020/ Saul Montoya

Development of open source software brings amazing new tools in all fields. In hydrogeology and groundwater modeling there is an increasing number of specific open source software and programming packages. We wanted to compile the latest libraries for Python related to hydrogeology, we asked for references and researched over the web to provide you the following list.

September 22, 2020

Extract point value from a raster file with Python, Geopandas and Rasterio - Tutorial

September 22, 2020/ Saul Montoya

This tutorial has a complete case of spatial analysis for the extraction of point data from a raster dataset with Python and its libraries Geopandas and Rasterio. The procedure is entirely geospatial and uses shapefiles and tifs as input data; data calculation was performed on a Jupyter Lab environment.

September 21, 2020

Developing geospatial webapps with Python and Django - Tutorial

September 21, 2020/ Saul Montoya

There are many ways to display spatial data, from the traditional maps, GIS desktop software and most recently on the web. We face certain challenges to display spatial data on the web because we will require certain functionalities that we find on a desktop software and certain spatial analysis tools implemented as buttons. Django is a web framework written in Python that allows to create web applications with moderate simplicity and this framework is capable of displaying vector spatial data using libraries such as Folium.

We have created a tutorial with an applied case of displaying hydrological spatial information on a webapp in Django. The tutorial creates a Django project, creates an app for the spatial data representation, imports the vector data (geojson or shp) and displays spatial data with defined styles.

September 01, 2020

How much does a groundwater model cost? And how long does it take?

September 01, 2020/ Saul Montoya

Development of groundwater numerical models on a commercial scale has brought some issues regarding stakeholder participation, prediction quality and indelible price and time.

It might be that the question of how much a model can cost can be resolved as an equilibrium of how much are people willing to pay and how much the consultant is willing to receive. We will discuss some topics of this critical but not well explained topic in this article.

August 30, 2020

Modeling impermeable walls with MODFLOW 6 and HFB Package - Tutorial

August 30, 2020/ Saul Montoya

Modeling the performance and effectiveness of flow barriers or impermeable walls on the groundwater flow regime is a challenge due to the wall geometry / orientation and discretization requirements. The package Horizontal Flow Barrier was designed to simulate barriers of defined thickness and conductances that are located in between flow cells, in this way the flow barrier is independent for the model discretization. This package is not new, it dates back to 1993, and it was implemented on many MODFLOW versions.

August 26, 2020

Hatarichem v2, the online tool to create Piper, Schoeller and Stiff Diagrams

August 26, 2020/ Saul Montoya

We present our own webapp for the representation of the Piper Diagram, Stiff Diagram and Scholler Diagram. The webapp was developed in Python Django and it is entirely free for everyone. The main objective behind this webapp was to develop a user friendly and minimum requirement tool to create these water quality / hidrogeochemical diagrams. The video tutorial shows the complete procedure to update the working file and then generate the diagrams.

August 24, 2020

Strategies for a hydrogeologist to develop advanced open source groundwater modeling software

August 24, 2020/ Saul Montoya

There are some shining moments in live where a normal hydrogeologist decide to develop open source software for groundwater modeling and for every great task everyone needs an strategy.

You might need a plan to develop your hydrogeological career but you will certainly need an strategy to develop groundwater modeling software. We have to see a strategy as the optimization of steps towards a goal, from great strategists as Hannibal Barca against the Roman empire, we need to see the whole picture and then decide the best steps to take with the resource available.

August 18, 2020

Why is the "first great experience" so important to learn open software in water resources?

August 18, 2020/ Saul Montoya

Software is a technology tool, and through the history of mankind, tools are most recent technology have changed our cognitive skills and developed our intelligence. Water resources specialists deal with numerical simulations of surface flow, groundwater flow, interaction with the environment and prediction of future impacts with an extensive use of software and computers. In our point of view, there is a need of professionals that can deal with many types of software and programming codes to develop comprehensive evaluations of the current and future conditions of the water resources.

August 09, 2020

Tutorial to create a geospatial Voronoi-sh mesh with Python, Scipy and Geopandas

August 09, 2020/ Saul Montoya

Divide a continuous media as a hydrological / hydrogeological basin into discrete parts is an art. Cell size have to related to hydrological features, cell number have to be optimized to cover areas of interest with an adequate refinement while minimizing the total cell number. The computational process has be fast to allow user run multiple times to achieve a desired mesh.

We have done a tutorial that creates a Voronoi-sh mesh over shapefiles with several options for refinement and polygon relaxation, resulting polygons are clipped to the mesh boundary and exported as shapefile or geojson. The script was done with Python, Scipy, and Geopandas.

July 17, 2020

Basic example of hydrological modeling at basin scale with HEC HMS 4.5

July 17, 2020/ Saul Montoya

HEC HMS is a software developed by the US Corps of Engineers that implements a series of hydrological methods to represent different physical process of the water cycle. The tools and options of HEC HMS make it a very versatile and powerful software for the hydrological simulation of different escenarios as extreme events on arid regions, or water balances in wet climates.

This tutorial shows the complete procedure to set up and simulate the hydraulic response of a 8 hour storms over a 20 hour period, model results are intended to show maximum flows and flow development with time. The area of study is a andean basin that was divided on two sub-basins (high and low part), each one has their own storm precipitation data. The model consider the use of hydrological components as subbasin, reaches and sinks.

July 15, 2020

Tutorial to run a simple model of OpenFOAM with Parafoam in Windows 10

July 15, 2020/ Saul Montoya

The following tutorial shows the procedure to run an example model with the simple solver (steady-state for incompressible turbulent flow) from OpenFOAM in Windows 10. The tutorial covers also the steps to install Xming for the direct visualization of the model output with Paraview.

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