January 11, 2018

How to plot MODFLOW Head Output in Paraview with Python - Tutorial

January 11, 2018/ Saul Montoya

MODFLOW computes the groundwater heads over a porous / fractured media upon a series of boundary conditions as recharge, evapotranspiration, drains, well and others on steady and transient conditions. Free and commercial software is available for the MODFLOW model construction and MODFLOW output representation. Despite the fact the capabilities of these softwares, there are some gaps in data processing and representation; isometric views, animation and custom cross sections are still difficult to achieve under the existing tools, specially on multilayered models with transient conditions over series of time steps and stress periods.

There is a particular open source software for data representation that is of our interest, it is called Paraview (paraview.org). This visual application was designed to analyze extremely large datasets using distributed memory computing resources, in fact the term "para" in Paraview comes from the parallelization of computer cores.

January 08, 2018

Introduction to GeoJSON and its advantages compared to ESRI Shapefile

January 08, 2018/ Saul Montoya

When dealing with spatial data for a project or a study sometimes the data format and data interoperatibility can be key to the success of the research or the map quality. For decades the ESRI Shapefile has been the most used format to exchange and to work with spatial data. From the Internet development a new geospatial data interchange format has been created to represent geographic features, their properties, and their spatial extends. This tutorial is a introduction to the GeoJSON data format with a practical work in QGIS 3 and a comparison of spatial data in both GeoJSON and ESRI Shapefile formats.

January 05, 2018

How to import a Water Table from MODFLOW in QGIS with Python - Tutorial

January 05, 2018/ Saul Montoya

Advances in groundwater modeling with MODFLOW allow us to have higher refinements on the representation of the water heads and water table as well as more capabilities in the representation of physical process related to groundwater flow. On a regional scale, we can deal with models of more than 500K elements and most times we need to represent this data on a GIS software for further study or the creation of figures for the end users, stakeholders and reports. By the use of Python scripts we can speed up the process of model output representation on a GIS software as QGIS.

Python scripts can be a little bit long and very declarative, but the process time is much smaller than the traditional clicking process on the GUI interface. The purpose is to store these scripts and use then every time one have to process the MODFLOW output data.

January 03, 2018

Fill Missing Precipitation Data with Artificial Intelligence (Python Keras) - Tutorial

January 03, 2018/ Saul Montoya

Evaluation of hydrological processes as evapotranspiration, runoff, routing and infiltration require data as precipitation, flow, temperature and radiation on a daily basis. Required data for the hydrological modeling need to be accurate and must be completed over the period of study. Many times historical data from hydrological stations are incomplete and present many gaps that can be filled by the use of Artificial Intelligence tools as the Keras library in Python.

This tutorial show the procedure to run a complete script for the filling of missing precipitation in one station by the use of data from 2 nearby stations. The Python script is done on a Jupyter Notebook.

December 29, 2017

Sedimentation Tank Design with OpenFOAM - Tutorial

December 29, 2017/ Saul Montoya

Drinking and residual water treatment, water intake into hydroelectric power stations or water treatment for industrial processes require the removal of suspended particles by sedimentation tanks. These hydraulic structures have a slow speed water inlet and a geometry that allows the decantation or precipitation of sediments along the settler path.

OpenFOAM is a open source software for Computational Fluid Dynamics (CFD) modeling with a series of solvers for different flow conditions. In this case we have used the driftFluxFoam solver to represent sediment precipitation in a sedimentator in a transient simulation of 6400 seconds. The tutorial contains 2 videos with the model description and its simulation.

December 25, 2017

Basic Example of a MODFLOW Model Creation and Simulation with Flopy - Tutorial

December 25, 2017/ Saul Montoya

Flopy is the Python library to create, run and represent results from MODFLOW models, including support for MODFLOW 6. With Flopy, the model definition and set up of boundary conditions can be done with lines of Python code, and some Python tools of optimization and machine learning can interact with the MODFLOW models. This tutorial show a basic example of model creation, configuration and simulation in Python 3 on a Jupyter Notebook. The tutorial also shows the procedure to import the MODFLOW results done with Flopy in Model Muse.

December 22, 2017

Crop Yield Assessment from Photos with Python and Scikit-Learn

December 22, 2017/ Saul Montoya

Evaluation of crop yield can be tedious because sampling methods requires the actual counting of fruits for a whole tree or canopy area. If we want to optimize this time demanding task we can use new and open source machine learning algorithms available. We have selected Scikit-Learn for this tutorial, a machine learning library in Python for it ease to use, the available documentation and the sort of available tools.

The tutorial covers the whole procedure of image representation, point of interest selection, template matching, cluster analysis and fruit counting. Python scripting was done in Jupyter Notebook, it is interactive and allows the user to add more points of interest or remove inaccurate points.

December 17, 2017

How to Convert a Matrix in a Geospatial Tiff in QGIS with PyQGIS - Tutorial

December 17, 2017/ Saul Montoya

Raster are matrices with geospatial reference. In order to make a finite difference model or any other model compatible with QGIS we have to process the matrix with its parameters to be represented as a spatially referenced raster. The process involves some Python scripting on the QGIS console, processing time is low and the process can be applied for many matrices without visual representation of intermediate files that saves computational time and resources.

This tutorial show the complete process of matrix construction, parameter calculation and spatially representation in the Python console of QGIS.

December 16, 2017

How to convert GTIFF to STL for Topography Representation in OpenFOAM Models

December 16, 2017/ Saul Montoya

For OpenFOAM modelers the representation of topography can be painful due to the unstabilities and complexities of the Bezier Surfaces in Salome Platform. It is more stable to create the mesh by importing a full textured surface on a format file compatible with Salome. This tutorial show the process to create a STL file from a GeoTiff(.tif) file by scripts in Python. We have used the OSGeo4W Shell that comes with the normal QGIS instalation because it comes with the gdal library already installed.

December 15, 2017

How To Create Line From Points in QGIS with PyQGIS and Pandas - Tutorial

December 15, 2017/ Saul Montoya

Python scripting allows us to enhance the data management and spatial analysis in QGIS. Most times, spatial data comes from a variety of data providers in a sort of formats and data types that we have to be adapted to the GIS standard. Big data and continuos monitoring create large datasets that have to indexed, sorted and manipulated in a effective way.

QGIS has a Python console and the capability to install external Python packages that run on QGIS session. This time we have installed Pandas in QGIS to handle the data from a sensing device made on a Raspberry Pi 3 and then we have defined the path as a succession of points with PyQGIS scripting.

December 12, 2017

Spatio-Temporal Hurricane Tracking in the Gulf of Mexico with QGIS and PyQGIS - Tutorial

December 12, 2017/ Saul Montoya

This tutorial show a mixed procedure with native QGIS tools and PyQGIS commands for the data representation, styling and plotting with spatio-temporal criteria with the TimeManager plugin. Data for this tutorial was downloaded from the National Hurricane Center's Tropical Cyclone Reports that contains information as six-hourly positions and intensities. You can access the whole hurricane database o

December 12, 2017

How to add multiple Vector Layers and group them in QGIS with PyQGIS - Tutorial

December 12, 2017/ Saul Montoya

QGIS is a great software for the processing/analysis of spatial data, Python is a clear, powerful programming lenguaje; together they can enhance the spatial analysis to solve more complex or more dedicated problems in less time. PyQGIS is the Python environment inside QGIS with a set of QGIS libraries plus the Python tools with the potential of running other powerful libraries as Pandas, Numpy or Scikit-learn.

This tutorial shows the whole procedure to upload multiple files from a certain pattern and group them on the Layer Panel using PyQGIS commands.

December 10, 2017

How to Upload a Shapefile in QGIS with PyQGIS - Tutorial

December 10, 2017/ Saul Montoya

December 04, 2017

Tree / Crop Counting and Classification with Python and Scikit-Image - Tutorial

December 04, 2017/ Saul Montoya

Lately there has been a wide source of spatial photogrametry available for agriculture. Available submetric images can be found in Google Earth, and drone images can increase the ortophoto resolution to the order of centimeters. Most of this data gives us a new perspective of the spatial distribution and stage of the crops, however a real spatial analysis of crop metrics have not been widely performed due to limitations on the images and software involved.

We tried to make this tutorial with the popular library OpenCV, however the installation process was tedious in Windows. Then we shifted to Scikit-Image, a image processing library in Python that comes already installed on the Anaconda software. The process for image analysis required intermediate Python and GIS skills, but most important a strong criteria of the algorithm inputs, options and results.

December 02, 2017

How to join tables in QGIS - Tutorial

December 02, 2017/ Saul Montoya

QGIS is a powerful open source software for spatial analysis and management of spatial data. User experience with QGIS is great and most users find QGIS easier to use than other free and commercial GIS software. This time we will show how simple is the process to join tables in QGIS. Spatial data of sanitary quality of beaches in Lima was used to show the join table process.

December 01, 2017

Groundwater Flow Simulation at Mine Closure Time Scale with MODFLOW and Model Muse

December 01, 2017/ Saul Montoya

This tutorial deals with the simulation of the groundwater flow regimen after the implementation of mine closure options as soil/geomembrane cover above a Tailings Storage Facility (TSF) over a period of 80 years with results every 4 years. The tutorial deal with a full steady flow model which have been implemented to transient conditions on the model configuration and boundary conditions. A discussion of the seepage with time and final conditions after closure is presented to analyse the efficiency of the closure techniques.

November 29, 2017

Example of Zone Budget Package in MODFLOW with Model Muse

November 29, 2017/ Saul Montoya

MODFLOW is the code developed by the USGS for the simulation of groundwater flow in steady and transient flow conditions. MODFLOW can represent a wide variety of physical process related to the groundwater flow regime as recharge, evapotranspiration, wells, among others. Latest development in MODFLOW allow the simulation of flow and transport in the unsaturated flow zone with the UZF and MT3D packages. From the beginning of the MODFLOW development the water balance on the groundwater models was a strong part of the modeling process with high accuracy in between the balance of water going in and out of the system. On any groundwater flow model build on MODFLOW there absolutely control over the water coming from the specified boundary conditions and the discrepancies are minimal.

November 23, 2017

Pathline Simulation of Seepage Flow from a Tailings Dam with MODFLOW & MODPATH - Tutorial

November 23, 2017/ Saul Montoya

Due to their extension and climate conditions, Tailings Storage Facilities (TSF) are in interaction with groundwater flow having a dual behaviour of discharge and recharge zones. Long term evaluation of environmental impact from tailings have to consider the potential impact from the leachates into the groundwater flow regime and the impact on water quality on the downstream channels. Numerical modeling is a strong tool for the evaluation of flows and quality on the overall impact zone from tailings dam in current and future conditions.

Simulations on mine closure last for decades, and several remediation techniques as infiltration ponds, pump and test schemes, reactive walls have to be simulated on the long term. This tutorial show the procedure to simulate the particle tracking of seepage flow from tailings and estimate the potential affected stream network. The tutorial also discuss some common problems in the particle tracking simulation.

Modeling work was done in MODFLOW with Model Muse on steady state conditions over a 5 layer model with 101260 cells.

November 16, 2017

Example of Particle Tracking Modeling with MODPATH in Model Muse

November 16, 2017/ Saul Montoya

MODPATH is a particle tracking model that runs on the groundwater flow models simulated on MODFLOW. Particle tracking are three dimensional and can have a sort of options as forward / backward modeling direction in between others. Model Muse is a pre and post-processor of numerical models in MODFLOW, PHAST and SUTRA, this software can simulate some MODFLOW related models as MODPATH and MT3D (particle tracking and mass transport respectively). This tutorial show the basic procedure to set up a particle tracking model with MODPATH using Model Muse over a basic MODFLOW model.

November 04, 2017

What is the relevance of confined / unconfined aquifer type on groundwater flow?

November 04, 2017/ Saul Montoya

Maybe confined or unconfined aquifer are terms that would sound familiar from your first hydrogeology class, however it´s a simple definition about the location of the hydraulic head over the vertical limits of your aquifer. It might be that you have employed those terms in different reports, or maybe you have seen this aquifer classification on some environmental impact assessments or geological reports, but which is the relevance of this classification on the groundwater flow? This article talks about the comparison of the the confined / unconfined aquifer condition based on numerical modeling with some discussion about the convertible character of the aquifer.