How to QGIS¶

Pre-processing with QGIS¶

To start any analysis of rivers and fluvial land scapes, a digital elevation model (DEM) is required. Nowadays, DEMs mostly are a result of light imaging, detection, and ranging (LiDAR) and bathymetric surveys. LiDAR employs lights sources and provides terrain assessments up to 2-m deep water. Deeper water requires additional bathymetric surveys with echo sounding methods. Merging LiDAR and bathymetric data produces point clouds that may be stored in many different file types. The first step in river modelling consist in the conversion of such point clouds into usable DEMs and computational meshes. This page guides through the conversion of a point cloud into a computational mesh with QGIS and the BASEmesh plugin. The descriptions refer to the developer’s documentation files (go to the ETH Zurich’s BASEMENt documentation).

Get ready with QGIS¶

Windows

Download and install the latest version of the open-access GIS software QGIS.

Linux

Make sure to install QGIS v3.16 via Flatpak or the Linux Software Manager (open Software Manager, search for QGIS and install the QGIS Flatpak). If Software Manager cannot find QGIS, make sure that Flatpak is added as repository (find the good repository for your Unix-based operating system (OS) here).
The QGIS Flatpak installation will most likely not include scipy. In order to fix this issue, open Terminal (standard application on Unix-based OS) and type: flatpak run --command =pip3 org.QGIS.QGIS install scipy --user.

This solution has been tested on Linux Ubuntu and Linux Mint. It potentially also works with Red Hat, openSUSE, Mac OS, Arch, Fedora, and roid, Debian, Kubuntu and many more. Read more about the QGIS Flatpak installation on the QGIS web site.

Start QGIS, create a new project and save it (Project > Save as...). Then, set the project coordinate reference system (CRS) by clicking on Project > Properties > CRS tab and select GERMANY_ZONE_3 (ESRI:31493). Install BASEMENT’s BASEmesh Plugin (instructions from the BASEMENT System Manual): 1. Load the QGIS plugin manager: Plugins menu > Manage and Install Plugins (see details in figure)

Go to the Settings tab; now the QGIS plugin repository connections should be visible at the bottom of the Plugin Manager (Plugin Repositories listbox in below figure).
Scroll to the bottom, click on Add…, and enter a name for the new repository (e.g., BASEmesh repository)
Enter the repository address: http://people.ee.ethz.ch/~basement/QGIS_plugins/QGIS_plugins.xml
Click OK. The new repository should now be visible in the Plugin Repositories listbox. If the connection is OK, click on the Close button on the bottom of the window.
Verify that the BASEmesh plugin is now available in the QGIS’ Plugins menu (see figure).

Fig. 27 Installation of the BASEmesh plugin.¶

Fig. 28 The BASEmesh plugin is available in QGIS’ Plugins menu after successful installation.¶

Elevation point data¶

Terrain survey data are mostly delivered in the shape of an x-y-z point dataset. LiDAR produces massive point clouds, which quickly overcharge even powerful computers. Therefore, LiDAR data may need to be break down to smaller zones of less than approximately 106 points and special LiDAr point processing software (e.g., http://lastools.org/) may be helpful in this task. The range of possible data products and shape from terrain survey is board and this tutorial exemplary uses a set of x-y-z points stored within a text file. Load the points from the provided xyz-points.txt file as follows:

Download the point file from the repository (if necessary, copy the file contents locally into a text editor and save the file as points.txt in a local project directory)
Download the zipped breaklines shapefile into the project folder and unpack breaklines.shp.
In QGIS, click on the Layer menu > Add Layer > Add Delimited Text Layer... (see figure)
In the Add Delimited Text Layer (Data Source Manager | Delimited Text) wizard (see details in Figure 4):
- Choose points.txt in the File name field (alternatively use points.csv)
- Name the new layer (e.g., points)
- In the File Format canvas, select Custom Delimiters and activate the Space checkbox
- In the Record and Field Options canvas, activate the First record has field names checkbox
- In the Geometry Definition canvas, define the Point Coordinates as X Field = X, Y Field = Y and Z Field = Z; set the Geometry CRS to the Project CRS.
- Click the Add button on the bottom of the wizard window. The points should now be plotted in the main QGIS window.

Fig. 29 Open the Add Delimited Text Layer import wizard.¶

Fig. 30 Load the xyz-points.txt file with QGIS’ Add Delimited Text Layer (Data Source Manager | Delimited Text) wizard.¶

Next, export the new point layer as shapefile: In QGIS’ Layers window, right-click on XYZ-POINTS, then Export > Save Features As... . In the Format field, select ESRI Shapefile. Define a FILE NAME (by clicking on the … button and defining for example C::raw-latex:`QGIS`-projects:raw-latex:`xyz`-points.shp), ensure that the ADD SAVED FILE TO MAP checkbox is activated (on the bottom of the Save Vector Layer As... window) and click OK. Remove the points text layer from the Layers window (only the shape file should be visible here now). Finally, rename the three fields (FIELD_1, FIELD_2, FIELD_3) to X, Y, and Z, respectively. The fields can be renamed with a double-click on the xyz-points layer (opens Layer Properties), then left-click on the Fields ribbon, activate the editing mode (click on the pen symbol) and edit the Name fields.

Model Boundary¶

The model boundary defines the calculation extent and needs to be define within a polygon shapefile that encloses all points in the above produced point shapefile. QGIS provides a Convex Hull tool that enables the automated creation of the outer boundary. This tool is used as follows:

In QGIS’ Processing menu, select Toolbox (see figure). The Toolbox sub-window opens now.
In the toolbox, click on Vector Geometry > Concave Hull (Alpha Shapes), which opens the Concave Hull (Alpha Shapes) wizard (see figure).
In the Concave Hull (Alpha Shapes) wizard, select the xyz-points layer as Input Layer, set the Threhold to 0.300 (keep default), define an output Concave Hull shapefile (e.g., boundary.shp) by clicking on the ... button, and click on Run.

Fig. 31 Open QGIS’ Toolbox from the main menu.¶

Fig. 32 The Concave Hull (Alpha Shapes) wizard.¶

Right-click on QGIS’ Settings menu, and activate the Snapping toolbar checkbox. In the now shown snapping toolbar, activate snapping with a click on the horseshoe icon.
Adapt the boundary.shp polygon to a tighter fit of the shapefile nodes by clicking on the Toggle editing (pen) symbol and activating the Vertex Tool in the toolbar.

Fig. 33 Toggle editing and enable the Vertex Tool.¶

Modify the boundary edges (as shown in figure): click on the centre cross (creates a new point) and dragging it to the next outest boundary point of the DEM points. Note:
- The boundary polygon must not be a perfect fit, but it must include all xyz-points with many details in vicinity of the river inflow and outflow regions (dense point cloud in the left part of the point file).
- The more precise the boundary the better will be the quality mesh and the faster and more stable will be the simulation.
- Regularly save edits by clicking on SAVE Layer (floppy disk symbol next to the editing pen symbol).

Fig. 34 Modify the boundary polygon with a click on the centre cross (creates a new point) and dragging it to the next outest boundary point of the DEM points.¶

Fig. 35 The final boundary (hull of the point cloud).¶

Breaklines¶

Breaklines indicate, for instance, channel banks and the riverbed, and need to coincide with DEM points (shapefile from above section). Breaklines a stored in a line (vector) shapefile, which is here already provided (breaklines.shp). Integrate the breaklines file into the QGIS project as follows with a click on QGIS’ Layer menu > Add Vector Layer... and select the provided breaklines.shp file (if not yet done, download and unpack the shapefile). Note: The default layer style Single Symbol. For better representation, double-click on the breaklines layer, got to the Symbology ribbon and select Categroized (or Graduated) instead of Single Symbol (at the very top of the Layer Properties window). In the Value field, select type, then click the classify button on the bottom of the Layer Properties window. The listbox will now show the values bank, bed, hole, and all other values. Change color pattern and /or click OK on the bottom-right of the Layer Properties window.

TIN Elevation Model¶

This section explains the creation of a triangulated irregular network (TIN) with the QGIS plugin BASEmesh (make sure that all steps in the above section were successful).

To start, click on QGIS’ Plugins menu > BASEmesh > Elevation Meshing to open the mesh wizard. (see also figure)
Model boundary = boundary layer (see above section)
elevation points = xyz-points (see above section)
Enable the breaklines checkbox and select the breaklines layer (see above section)
In the Shapefile outputcanvas, click on the BROWSE button and save the new file as, for example, base_tin.shp.
Click on Generate Elevation Mesh and Close the wizard after successful execution.

As a result, two new layers will now show up in the Layers window:

base_tin_elevation_nodes.shp, and
base_tin_elevation_elements.shp.

Fig. 36 Setup BASEmesh’s Elevation Meshing wizard.¶

Region Markers for Quality Meshing¶

Region markers are placed within regions defined by breaklines and assign for instance material identifiers (MATIDs) and maximum mesh areas to ensure high mesh quality (e.g., the mesh area should be small in the active channel bed and can be wider on floodplains). To create a new region marker file:

Click on QGIS’ Layers menu > Create Layer > New Shapefile Layer... (see figure)

Fig. 37 Create a new point shapefile for region definitions from QGIS’ Layer menu.¶

In the newly opened New Shapefile Layer window, make the following definitions (see also figure).
Define the File name as region-points.shp (or similar)
Ensure the Geometry type is Point and the CRS corresponds to the above definitions (see above section).
Add four New Fields (in addition to the default Integer type ID field): + max_area = Decimal number (length = 10, precision = 3) + MATID = Whole number (length = 3) + type = Text data (length = 20)
Click OK to create the new point shapefile.

Fig. 38 Definitions and fields to be added to the new regions point shapefile.¶

After the successful creation, right-click on the new REGION-points layer and select TOGGLE EDITING. Then go to QGIS’ EDIT menu and select ADD POINT FEATURE. Create 9 points to define all areas delineated by the breaklines layer. These points should include the following region types:

Type	riverbed	lower_bank	upper_bank	floodplain	street
`MATID`	1	2	3	4	5
max_area	25.0	50.0	100.0	400.0	100

The below figure shows an example for defining points within the areas delineated by the breaklines.

Fig. 39 Example for distributing region points in the project boundaries (remark: the max_area value may differ and is expert assessment-driven). After the placement of all region points, Save Layer Edits (floppy disk symbol) and Toggle Editing (pencil symbol – turn off).¶

Quality meshing¶

A quality mesh accounts for the definitions made within the regions shapefile (see above section), but it does not include elevation data. Thus, after generating a quality mesh, elevation information needs to be added from the TIN (see above section). This section first explains the generation of a quality mesh and then the insertion of elevation data).

Quality mesh generation¶

In QGIS’ Plugins menu, click on BASEmesh > QUALITY MESHING to open the Quality meshing wizard. Make the following settings in the window (see also figure):

Model boundary = boundary (see above section)
breaklines = breaklines (see above section)
Regions = regions-points (see above section) and activate all checkboxes
In the Shapefile output canvas, click on the browse button to define the output mesh as (for example) base_qualitymesh.shp

Fig. 40 BASEmesh’s Quality Meshing wizard.¶

Quality meshing may take time. After successful mesh generation the files base_qualitymesh_qualityNodes.shp and base_qualitymesh_qualityElements.shp are generated. Finally, click Close.

Elevation data interpolation on a quality mesh¶

BASEmesh’s Interpolation wizard projects elevation data onto the quality mesh by interpolation from a TIN. Make sure to check (show) the base_qualitymesh_qualityNodes and base_qualitymesh_qualityElements from the last step, and base_tin_elevation_nodes.shp and `base_tin_elevation_elements.shp <#tin>`__. Then, open BASEmesh’s Interpolation wizard (QGIS Plugins menu > BASEmesh > Interpolation) and (see also figure):

In the Quality Mesh canvas, select base_qualitymesh_qualityNodes
In the Elevation Data canvas, activate the Elevation Mesh checkbox and select base_tin_elevation_nodes.shp and `base_tin_elevation_elements.shp <#tin>`__
In the Shapefile output canvas, define the output file as finalmesh.shp.
Click Interpolate elevations (may take a while) After successful execution, the new layer finalmesh_Interpolated_nodes_elevMesh.shp will be created. Click Close to close the Interpolation wizard.

Fig. 41 BASEmesh’s Interpolation wizard and setup.¶

Verify quality mesh elevation¶

After the elevation interpolation, verify that elevations were correctly assigned. To identify potential outliers double-click on the new finalmesh_interpolated_Nodes_elevMesh and go to the Symbology ribbon. Select Graduated at the very top of the window (instead of Single Symbol), set the Value to Z, METHOD to COLOR, choose a color ramp, and click on the classify bottom (lower part of the window). Click on Apply and OK to close the Symbology window. The below figure shows an example of interpolated mesh, with some irregularities (red points). The irregularities are caused by local imprecision of breaklines (line end points do not coincide with the `xyz-points.shp <#epd>`__). Also some points of the boundary do not correspond the xyz-points.shp. If such irregularities occur, zoom at the red points (irregularities) and ensure that the breakline and boundary nodes all exactly coincide with those stored in xyz-points.shp. When all nodes are corrected, repeat all steps from the TIN generation onward.

Fig. 42 Verify elevation interpolation using graduated color ramps. In this example, the red colored points indicated irregularities in the mesh.¶

Export to 2dm¶

To run BASEMENT, the mesh needs to be exported in 2dm format. BASEmesh’s Export Mesh wizard (QGIS Plugins menu > BASEmesh > Export Mesh) does the job with the following settings (see also below figure: Export of the mesh to 2dm format with BASEmesh’s Export Mesh wizard.):

Select the checkbox 2d MESH Export
Mesh elements = base_qualitymesh_quality_elementy.shp (see above) with Material ID field = MATID
Mesh nodes = finalmesh_interpolated_nodes_elevmesh.shp (see above) with Elevation field =Z
In the Mesh output canvas, click on the Browse button and select an export mesh directory and name (e.g., finalmesh.2dm).
Click on Export Mesh (may take a while) and Close the wizard afterwards.

Fig. 43 Export of the mesh to 2dm format with BASEmesh’s Export Mesh wizard.¶

In order to work with BASEMENT v3.x, the .2dm file requires a couple of adaptations. Open the produced finalmesh.2dm in a text editor software (right-click and , for example, edit with Notepad++) and :

At the top, insert the following line at line No. 2: NUM_MATERIALS_PER_ELEM 1

Fig. 44 Modification of the upper part of the .2dm file.¶

At the bottom of the file, add the node string definitions for the inflow and outflow boundary. Enter the following 2 new lines (where ndi and ndj represent the Inflow and Outflow nodes, respectively, of finalmesh_interpolatedNodes_elevMesh.shp):
- NS[SPACE][SPACE]nd1[SPACE]nd2[SPACE]ndi[SPACE]ndn[SPACE]Inflow
- NS[SPACE][SPACE]nd1[SPACE]nd2[SPACE]ndj[SPACE]ndm[SPACE]Outflow

Tip

To identify the node IDs open QGIS use BASEmesh’s Stringdef wizard (from BASEMENT v2.8 user manual - read more below).

Stringdef identifies points that have a non-empty stringdef-field (i.e., all nodes that are located exactly on that line) and writes them into a text file (BASEMENT-like stringdef block). The content of the stringdef-field represents the stringdef name.
In order to identify the node ids on the inflow and outflow boundary lines, select the final mesh nodes in the Mesh Nodes dialogue, select the provided breaklines shapefile in the Breaklines dialogue and select stringdef from the dropdown menu.
In the Textfile OUTPUT dialogue, select an output text file (e.g., C:/temp/stringdef-breaklines.txt) and click on Find node IDs

Fig. 45 BASEmesh’s Stringdef tool.¶

The Stringdef tool now has generated stringdefs in upstream-looking right direction (note: to create new boundaries, the lines need to be drawn from the left riverbank to the right riverbank).
Open the resulting text file (C:/temp/stringdef-breaklines.txt in the above example) and copy the node list to the bottom of finalmesh.2dm with the above-shown format (i.e., start with NS, followed by two SPACEs, then the node IDs ndi/j * separated by on SPACE, then *Inflow and Outflow, respectively). Note: The node IDs my vary from those shown in the figure(s).

Finally, the bottom of the finalmesh.2dm (text editor) should look like this in the text editor (node IDs may vary from those in the screenshot):

Fig. 46 Modification of the bottom part of the .2dm file.¶

Congratulations, you finished meshing!

Hydro-Informatics