February 04, 2020

How to translate Coordinate Systems for XY Point Data tables with Python Pandas and Pyproj

February 04, 2020/ Saul Montoya

Spatial information is linked to the position and a system of reference. There are many coordinate systems worldwide with different length units, projections and origins. Somehow, spatial analysis is always linked to information stored on different coordinate systems and we have to provide effective ways to translate them to a specific CRS (coordinate reference system).

We have developed a tutorial for the coordinate system translation of XY point location stored in tables. The tutorial shows the procedure to change coordinate systems from geographic and planar coordinates using the Pyproj library over a Pandas dataframe on a Jupyter notebook.

December 18, 2019

How to smooth a Aster DEM elevation raster with QGIS 3 - Tutorial

December 18, 2019/ Saul Montoya

In developed parts of the world there are online elevation repositories with current and historical elevation data from field surveys, lidar, etc. However, for the rest of the world, the availability of online resources for elevation with adequate resolution are scarce. The ASTER Global Digital Elevation Model 1 arc second (ASTGTM v003) is one of the most reliable sources for elevation worldwide with a cell resolution of 30m and interpreted from "recent" images (from 2000 to 2013). In flat or vegetated areas the procedure to interpreted elevations face some complexities and the Aster DEM images show some bumps or high elevation spots that are not coherent when contrasting the elevation model with satellite panchromatic images. This tutorial shows a procedure to smooth the Aster elevation models with standard QGIS 3 tools on a practical exercise over a study area. The procedure can be applied to Alos Palsar images or any other noisy elevation raster.

December 06, 2019

Fault Zone Groundwater Flow Modeling with MODFLOW6 DISV and Model Muse -Tutorial

December 06, 2019/ Saul Montoya

Conceptualization and simulation of groundwater flow in the area of influence of geological faults is really a challenge for numerical modelers. Besides the complexities and variety of faults there were some limitations of the numerical codes to simulate the mixed behaviour of faults and altered zones. We have developed an example tutorial to represent the main characteristics of groundwater flow in the fault zone for an applied case. The tutorial is developed in Model Muse with the MODFLOW DISV option for unstructured grid generation. Groundwater flow was analyzed on the water balance and a particle tracking simulation was done with MODPATH 7.

December 02, 2019

How to create an Elevation Raster from Contour Lines with Python, Geopandas, Numpy and Gdal - Tutorial

December 02, 2019/ Saul Montoya

Spatial analysis is such an interesting discipline because it allows the evaluation of every phenomena related to their location. However, for some parts of the data processing the workflow on a GIS Graphical Computer Interface (GUI) can be repetitive and time consuming. Researchers need better and more efficient tools to process more amount of data in less amount of time and even with less quantity of software tools.

We have create a innovative script to generate an elevation raster file from a contour line with several steps of data processing. The script recognizes invalid geometries, simplify the polylines and extract vertices while creates a point geodataframe that is interpolated and geotransformed as a geospatial raster in .tiff format.

November 29, 2019

How to define cell / layer confinement in MODFLOW 6 with Model Muse

November 29, 2019/ Saul Montoya

The process and options to define the cell / layer confinement has changed in MODFLOW 6 with respect to MODFLOW 2005. We have done an explanatory video about the process to setup the confinement for cells in MODFLOW 6 with Model Muse. There is also a discussion on the influence of the confined / convertible option on the aquifer response on an example model.

November 25, 2019

Produced Water Chemistry and Isotope Analysis with Python and Pandas - Tutorial

November 25, 2019/ Saul Montoya

On hydrocarbon extraction, water is a byproduct that comes from the geologic formations that have also oil and gas. Produced water can be defined as fossil water, or water with a high residence time on the earth, with a particular water chemistry that is important to analyze when we deal with the treatment methods, disposal techniques or safety to drinking water sources. The USGS has developed a produced water geochemical database with more than 100K points that includes spatial information, well description, rock properties, water chemistry and isotopes.

November 18, 2019

Basic Example of Stream Flow Routing (SFR) Package with MODFLOW and Model Muse

November 18, 2019/ Saul Montoya

The disconnexion of surface groundwater flow it is fact very common on highly exploited aquifers or under impacts from climate change. Many rivers are disconnected from the groundwater flow regime decreasing their flow amount due to infiltration losses. For the simulation of this surface flow, unsaturated flow and groundwater flow phenomena the MODFLOW package Streamflow Routing (SFR) was developed.

This tutorial develops an numerical model of disconnected surface groundwater flow with MODFLOW SFR and Model Muse. The study case has regional flow and a river network with monthly flow on transient conditions over 2 years.

November 06, 2019

Geochemical Speciation Modeling and Analysis with Phreeqc and Julia - Tutorial

November 06, 2019/ Saul Montoya

The speciation modeling allows to calculate the distribution of aqueous species in a solution. Phreeqc is capable to simulate this speciation calculation and we are going to demonstrate this capability on a study case of aqueous species in seawater. Modeling was done with a Phreeqc executable and results were analysed on a interactive Julia script. Both parts were done on a Jupyter Lab session.

October 25, 2019

Websites where you can download complete groundwater flow models in MODFLOW

October 25, 2019/ Saul Montoya

Learning groundwater modeling is a challenge for the complexities of the codes, the lack or scarce piezometric and water quality data, the heterogeneity of the porous media and the few resources to explore complete and applied groundwater models with different boundary conditions and predictive scenarios.

Just few websites had uploaded complete groundwater flow models in MODFLOW and are accessible to the general public. We have to admit that most of the websites come from public institutions in the US. We hope that in a near future we can have more resources to get model reports and the complete MODFLOW model.

October 18, 2019

Introducing Hataripy, the unofficial Flopy version that creates awesome VTKs

October 18, 2019/ Saul Montoya

A new unofficial version of the Flopy is available as Hataripy. This “fork” has tools for the representation of many features, boundary conditions and output with options for grid smoothing. Documentation for this library is on progress as we expect to introduce other features and identify some bugs.

Currently the library can:

Create the model mesh on the active zone with point and cell values
Create a shell of the water table
Create the geometry of any boundary condition

October 02, 2019

Unofficial MODFLOW flow and transport executables for Linux (Ubuntu tested)

October 02, 2019/ Saul Montoya

It might be that you are a talented groundwater modeler and very proficient with Python and Flopy that you start to realize that you don´t need to work in Windows anymore and want to migrate your favorite groundwater modeling code to other nice, soft, and warm Linux-based operating systems. Or, it might be the case that you want to configure and run MODFLOW models as a part of a webapp or in a web server. For the reasons mentioned before and other reasons that modern world could bring to us, a compiled version of MODFLOW in Linux is needed.

September 02, 2019

How to fill missing Elevations to empty Contour Lines with PyQGIS

September 02, 2019/ Saul Montoya

Elevation contour lines without the elevation attribute is common when we import contour lines from Autocad DXF files, but it has also happened that contour data was stored on a hard disk drive without elevation attribute and years later data is found and there is no one to ask to restore the missing information. This tutorial shows a practical procedure to fill missing elevations on contour lines with the use of PyQGIS on QGIS 3. The procedure uses an intersection line that crosses the contour lines where the base elevation and interval is known. There are some specific instructions to run the script that are well described on the video.

August 13, 2019

Temporal discretization impact on MODFLOW Model Heads and Water Budget

August 13, 2019/ Saul Montoya

For a transient model, a modeler needs to conceptualize a coherent and feasible time discretization approach, nevertheless searching for temporal discretization guidelines the Internet gives you digital noise: nothing relevant, nothing precise, nothing useful. These is the type of situation where you ask yourself: how many stress periods do I need, how many time steps do I require, which should be an appropriate size of the model output, or more important, will the size and number of stress periods and time steps have an effect on the model output?

August 08, 2019

How to Convert a PDF to ESRI Shapefile with Python, Geopandas and Inkscape - Tutorial

August 08, 2019/ Saul Montoya

In order to use the spatial data provided on a report we need procedures to extract the data on effective way. The amount of tools and techniques are quite advanced, and requires several open source software for specific procedures. We have done a complete tutorial with all the step required to extract the vector spatial data of a map reported as PDF into a ESRI shapefile. For this tutorial we have used Inkscape for the conversion of the PDF to DXF, QGIS to extract some information of the DXF, Python and Geopandas on a Jupyter Lab session for spatial translation and scaling.

July 24, 2019

The dark side of Python for Hydrology / Hydrogeology and the nightmare of unmet dependencies

July 24, 2019/ Saul Montoya

The near future of data processing for Hydrology / Hydrogeology is written in Python 3, and many universities and institutions are shifting from teaching C++, Matlab or Fortran to Python. It is surprising the amount of tools, packages, codes and Ipython notebooks available for the data processing and data analysis of water related data, even with high success in data analysis reproducibility.

However, there is not always a sunshine on working with Python, especially if you are working on Windows. After you have done your first steps in hydrological series plotting, statistical analysis or even run a neural network, you might want to do more with Python and there is when the situation can become unbearable.

July 15, 2019

How to do more Groundwater Modeling (or any modeling) in less amount of time

July 15, 2019/ Saul Montoya

Because time matters and everybody wants results and solutions now, groundwater modelers (or any water resources modeler) have to think how they can do more with the limited time available. This is a restructuration, a reengineering, a new conceptualization of not only what we do, but how we do, and if in the end we are happy with the main results, and secondary results we get from our modeling work.

Groundwater modelers are water resources specialists with high skills in computing, coding, maths and groundwater flow regime comprehension. The type of work, the complexity of the given areas of study, the limited observation data, the limited budget, the short completion times and the overall low perception and low understanding of groundwater flow and groundwater quality makes the modeling work somehow particular where we have to adopt special techniques to deliver good work while preserving the modeler integrity and wellness.

July 09, 2019

The soft and hard courses every Applied Hydrogeology Master Program should have

July 09, 2019/ Saul Montoya

There isn’t as well a clear definition of applied hydrogeology, that following the literal meaning should be the hydrogeology in practice. We like the definition of applied hydrogeology as the real world hydrogeology, as the hydrogeology of non-homogeneous, non-infinite, non-isotropic and even non-porous media; applied hydrogeology is the hydrogeology that goes behind the book, far away from the “aquifer, aquitard, aquiclude” classification. Applied hydrogeology is the part of hydrogeology that solve problems, the science that tells us if the groundwater remediation will work, if a industrial complex will have water on the coming decade, or when the salinitization from the pumping well will overcome the reverse osmosis plant capacity.

July 08, 2019

6 aquifers that every hydrogeologist should visit on a lifetime

July 08, 2019/ Saul Montoya

Perception and interest on the groundwater resources are of high initial interest but long term low popularity, that is why normal and plain hydrogeologist need to promote an innovative perspective of the relation from human society with the groundwater resources as a strong part for every environmental protection plan and sustainable management policy elaboration.

This article has a list of aquifers around the globe, with special characteristics where a normal audience can see how water can exist below surface, how people have interacted with the aquifer

July 04, 2019

How to work with Transmissivities in MODFLOW with Model Muse - Tutorial

July 04, 2019/ Saul Montoya

Hydraulic parameters for an aquifer flow can be expressed on different terms like Hydraulic Conductivity (K) or Transmissivity (T). On the default setup of MODFLOW 2005 with Model Muse there is no option to use directly Transmissivity unless a manual conversion is done to transform into K, this is because the selected flow package is Layer Property Flow (LPF).

When the flow package changes to Block Centered Flow (BCF6) it is possible to insert Transmissivities directly as datasets or as a object property. The BCF package also has more options for the layer type, with unconfined and partial confined aquifer options.

July 03, 2019

Performance analysis of Open Drone Map to process hundreds of drone images

July 03, 2019/ Saul Montoya

So far, OpenDroneMap is a strong open source alternative for the processing of drone imagery. We have done a recursive analysis over a set of aerial photos on a standard desktop computer to have a panorama of the rates and trends from OpenDroneMap in the computation of different amount of images. Although the rates and trends apply only for a specific dataset and computer configuration, this study can to be taken as a reference for the computational time and as a perspective of how the software works with great amount of data.