Basic GRASS GIS with BASH, plus GDAL

As a follow-up to the last blog, I thought it would be helpful to demonstrate how next to break up the elevation example into individual watersheds. The reason being, in my last example I demonstrated the process using a square raster tile. Hydrological processes are not accurate when run on square tiles. It is best to run further processes, like stream order extraction, on complete watersheds.

If you are reading this and want to follow along, it is very helpful to go back and read this blog. The following builds off that last example.

I’ll break this into two parts:

1. Creating multiple watershed boundaries of different sizes with GRASS and using a basic loop in BASH for the process.
2. Clipping the original raster by the watershed boundaries using GDAL and SQL with a basic loop in BASH.

Creating Watershed Boundaries with Varying Sizes

This section will modify the script created in the last post.

Notice in the previous script, when I used r.watershed, I set the threshold value to 100000. You can use this value to set the minimum size of your watershed based on cell units. I see this as minimum number of pixels per watershed since your cell unit is the size of your pixel.

r.watershed elevation=$fillDEM threshold=$threshold accumulation=$accumulation drainage=$drainage stream=$stream basin=$basin --overwrite

Have a play setting the threshold value to different values, like 2000000 or 5000. You will get very different outputs in your watersheds vector layer. Try to determine the upper most threshold value you can input before GRASS can no longer determine a watershed.

Warning: really small threshold values will take very long to process and give very poor results, like thousands of very tiny watersheds of little to no value in analysis.

Once you have found you upper most limit for you threshold, determine a few lesser values and build them into a list. Maybe take the upper limit, half it, then half it again.

Make that into a list into a variable:

$ list=$(echo 2000000 1000000 500000)

Then loop the list to iterate through your threshold values when running r.watershed in GRASS. All we change from the last script is the threshold value to use the item from the list. Note we add the threshold value as part of the name too.

Use the standard form of a BASH loop:

for i in $list
    echo $i 

Loop with GRASS watershed commands:

list=$(echo 2000000 1000000 500000)

for i in $list
    # Run watershed operation on fill sink raster
    r.watershed elevation=$fillDEM threshold=$threshold accumulation=$accumulation drainage=$drainage stream=$stream basin=$basin --overwrite

    # Convert Basin (watershed) to vector format
    basinVect=${rasterName}_basinVect_${i} input=$basin output=$basinVect type=area column=bnum --overwrite

    # Export catchment to vector format
    v.out.ogr input=$basinVect output=$basinVectOut type=area format=ESRI_Shapefile --overwrite

Full script example here

Your outputs this time will be a collection of shapefile watersheds constructed by your threshold value.

Clipping your Raster by Individual Watersheds using GDAL, OGR and SQL

The watersheds layers are full of nice watersheds, however you cannot simply clip the elevation raster by the full vector file. For the clip, you need to select each individual watershed first. The following will demonstrate how to list each of those watersheds and use them as a clip file via a loop.

To start, set up a test directory for your processed raster outputs:

$ mkdir grass_test/raster_watersheds

The basic command for clipping a raster with a vector in GDAL is:

$ gdalwarp -of GTiff -cutline input_shapefile_for cut.shp input_raster_to_be_cut.tif output_raster.tif

You could create a shapefile for each watershed and clip your raster by that watershed individually using the command above, but the process would be fraught with errors and take a very long time.

It is much easier to automate the process using a combination of ogrinfo, sql and gdal.

We’ll do this with an example using JM_basinVectOut_2000000.shp you just created.


In the example, we’ll:

1. Read and list individual watersheds from the vector layer, by listing all the ‘cat’ values leveraging the ogrinfo -sql switch.
2. Using the list, we’ll clip the original raster by each individual watershed

First, list the ‘cat’ values in the vector watershed layer.

The basic ogrinfo command is:

$ ogrinfo /grass_test/JM_basinVectOut_2000000.shp

For this operation; however, we need to list the information of each row in the attributes:

$ ogrinfo -geom=NO -q -sql "SELECT cat FROM JM_basinVectOut_2000000" /grass_test/JM_basinVectOut_2000000.shp

In the above ogrinfo command lists all of the rows for the ‘cat’ column, excluding any geographic information for the file. To do this we use the ‘-sql’ switch available in ogrinfo.

Note when using the ‘-sql’ switch you need a layer name, ‘JM_basinVectOut_2000000’ from the shapefile. The layer name is just the name of the shapefile with the .shp removed.

Use grep to select the parts from the output you want and sed to clean up the outputs for a tidy list.

$ ogrinfo -geom=NO -q -sql "SELECT cat FROM JM_basinVectOut_2000000" /home/ireese/grass_test/JM_basinVectOut_2000000.shp | grep 'cat (Integer)' | sed s/'cat (Integer) =//g'

Make it a list variable:

$ watershedList=$(ogrinfo -geom=NO -q -sql "SELECT cat FROM JM_basinVectOut_2000000" /home/ireese/grass_test/JM_basinVectOut_2000000.shp | grep 'cat (Integer)' | sed s/'cat (Integer) =//')

Before we loop the process in gdal lets look quickly at why this list was created.

In gdalwarp we are going to again leverage the ‘-sql’ switch in order to select each individual watershed row and clip only by that row. We’ll be writing the a basic ‘sql’ similar to the above, but instead filtering by each watershed:

SELECT cat FROM watershed WHERE cat=$i

So, putting all the bits together, using clip and SQL, in gdalwarp we get:

$ gdalwarp -of GTiff -dstnodata -9999 -cutline $inputVector -csql "SELECT cat FROM $inputVectorLayerName where cat='$i'" -crop_to_cutline input_raster_to_be_cut.tif output_raster.tif

Note, I am using ‘-crop_to_cutline’ and ‘-dstnodata’. Basically I’m saying, crop the output raster the bounding box of the input vector and set a ‘nodata’ value of -9999 to the pixels outside the clip area.

Now we need put this all together in a script to loop the process.


# set base path

# Set raster as variable
rasterName=$( basename $raster | sed 's/.tif//g' )

#prep your input vectors
inputVectorLayerName=$(basename $inputVector | sed 's/.shp//')

#create your watersheds list
watershedList=$(ogrinfo -geom=NO -q -sql "SELECT cat FROM $inputVectorLayerName" $inputVector | grep 'cat (Integer)' | sed s/'cat (Integer) = //')

for i in $watershedList
    gdalwarp -of GTiff -dstnodata -9999 -cutline $inputVector -csql "SELECT cat FROM $inputVectorLayerName where cat='$i'" -crop_to_cutline $raster $outDirRast/${rasterName}_${i}.tif

Copy the above script, check your file paths, and save it in a text editor as:


To run the script:

$ bash grass_test/

Final Note
In the above process, it may be necessary to run some clean up operations to remove invalid geometries in the watersheds vector layer. I did not include this, but it is helpful to resave the watersheds shapefile first by running a buffer operation with a buffer value of ‘0’. This will remove the invalid geometries. You can run this in GRASS or using ogr2ogr with PostGIS. Here is an ogr2ogr with PostGIS example:

$ ogr2ogr -f "ESRI Shapefile" output_vector.shp input_vector.shp -dialect sqlite -sql "select id, ST_buffer(Geometry,0) as geom from input_vector" -overwrite

All the scripts from the past two posts can be found here.

Let me know of this helpful. I could potentially move on to doing some more basic hydro analysis with GRASS and BASH, but these things take time and energy. It would be good to know if these sorts of blogs have value to the wider geospatial world.